1
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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2
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Zhang Z, Khanal N, Dykstra AB, Daris K. Stop-Codon Readthrough in Therapeutic Protein Candidates Expressed from Mammalian Cells. J Pharm Sci 2024; 113:1498-1505. [PMID: 38342339 DOI: 10.1016/j.xphs.2024.02.006] [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: 01/02/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Stop codon readthroughs were examined in 48 recombinant therapeutic protein candidates produced from multiple clones of Chinese hamster ovary cells, using peptide mapping with LC-MS/MS detection. We found that stop codon readthrough is a common phenomenon occurring in most of these candidates, with levels varying from below the detection limit of ∼0.001 % to ∼1 %. The readthrough propensity depends on the stop codon being used, as well as the nucleotides surrounding it. The amino acids misincorporated into the stop position can be well-predicted by a third-base wobble mismatch and a first-base U/G mismatch during codon recognition, i.e., tyrosine or glutamine insertion for the UAA and UAG stop codons, and tryptophan, cysteine or arginine insertion for the UGA stop codon. Data shown in this report demonstrate the importance of optimizing the DNA sequence near the stop codon, and the importance of detecting stop codon readthroughs during the development of a therapeutic product.
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Affiliation(s)
- Zhongqi Zhang
- Process Development, Amgen Inc. Thousand Oaks, CA 91320, USA.
| | - Neelam Khanal
- Process Development, Amgen Inc. Thousand Oaks, CA 91320, USA
| | | | - Kristi Daris
- Process Development, Amgen Inc. Thousand Oaks, CA 91320, USA
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3
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Turnbull K, Paternoga H, von der Weth E, Egorov AA, Pochopien AA, Zhang Y, Nersisyan L, Margus T, Johansson MJ, Pelechano V, Wilson DN, Hauryliuk V. The ABCF ATPase New1 resolves translation termination defects associated with specific tRNA Arg and tRNA Lys isoacceptors in the P site. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596377. [PMID: 38854126 PMCID: PMC11160720 DOI: 10.1101/2024.05.29.596377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.
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Affiliation(s)
- Kathryn Turnbull
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen, Denmark
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Esther von der Weth
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Artyom A. Egorov
- Department of Experimental Medicine, University of Lund, 221 84 Lund, Sweden
| | - Agnieszka A Pochopien
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Lilit Nersisyan
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | | | | | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, 221 84 Lund, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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4
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Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough. Nat Commun 2024; 15:4446. [PMID: 38789441 PMCID: PMC11126739 DOI: 10.1038/s41467-024-48387-x] [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: 02/22/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Anastasiia Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Tobias Jumel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
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5
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Lebeda D, Fierenz A, Werfel L, Rosin-Arbesfeld R, Hofhuis J, Thoms S. Systematic and quantitative analysis of stop codon readthrough in Rett syndrome nonsense mutations. J Mol Med (Berl) 2024; 102:641-653. [PMID: 38430393 PMCID: PMC11055764 DOI: 10.1007/s00109-024-02436-6] [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: 10/13/2023] [Revised: 01/16/2024] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder resulting from genetic mutations in the methyl CpG binding protein 2 (MeCP2) gene. Specifically, around 35% of RTT patients harbor premature termination codons (PTCs) within the MeCP2 gene due to nonsense mutations. A promising therapeutic avenue for these individuals involves the use of aminoglycosides, which stimulate translational readthrough (TR) by causing stop codons to be interpreted as sense codons. However, the effectiveness of this treatment depends on several factors, including the type of stop codon and the surrounding nucleotides, collectively referred to as the stop codon context (SCC). Here, we develop a high-content reporter system to precisely measure TR efficiency at different SCCs, assess the recovery of the full-length MeCP2 protein, and evaluate its subcellular localization. We have conducted a comprehensive investigation into the intricate relationship between SCC characteristics and TR induction, examining a total of 14 pathogenic MeCP2 nonsense mutations with the aim to advance the prospects of personalized therapy for individuals with RTT. Our results demonstrate that TR induction can successfully restore full-length MeCP2 protein, albeit to varying degrees, contingent upon the SCC and the specific position of the PTC within the MeCP2 mRNA. TR induction can lead to the re-establishment of nuclear localization of MeCP2, indicating the potential restoration of protein functionality. In summary, our findings underscore the significance of SCC-specific approaches in the development of tailored therapies for RTT. By unraveling the relationship between SCC and TR therapy, we pave the way for personalized, individualized treatment strategies that hold promise for improving the lives of individuals affected by this debilitating neurodevelopmental disorder. KEY MESSAGES: The efficiency of readthrough induction at MeCP2 premature termination codons strongly depends on the stop codon context. The position of the premature termination codon on the transcript influences the readthrough inducibility. A new high-content dual reporter assay facilitates the measurement and prediction of readthrough efficiency of specific nucleotide stop contexts. Readthrough induction results in the recovery of full-length MeCP2 and its re-localization to the nucleus. MeCP2 requires only one of its annotated nuclear localization signals.
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Affiliation(s)
- Dennis Lebeda
- Department for Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Adrian Fierenz
- Department of Child and Adolescent Health, University Medical Center Göttingen, Göttingen, Germany
| | - Lina Werfel
- Department of Child and Adolescent Health, University Medical Center Göttingen, Göttingen, Germany
- Present Address: Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Julia Hofhuis
- Department for Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Sven Thoms
- Department for Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany.
- Department of Child and Adolescent Health, University Medical Center Göttingen, Göttingen, Germany.
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6
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Premchandar A, Ming R, Baiad A, Da Fonte DF, Xu H, Faubert D, Veit G, Lukacs GL. Readthrough-induced misincorporated amino acid ratios guide mutant-specific therapeutic approaches for two CFTR nonsense mutations. Front Pharmacol 2024; 15:1389586. [PMID: 38725656 PMCID: PMC11079177 DOI: 10.3389/fphar.2024.1389586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Premature termination codons (PTCs) represent ∼9% of CF mutations that typically cause severe expression defects of the CFTR anion channel. Despite the prevalence of PTCs as the underlying cause of genetic diseases, understanding the therapeutic susceptibilities of their molecular defects, both at the transcript and protein levels remains partially elucidated. Given that the molecular pathologies depend on the PTC positions in CF, multiple pharmacological interventions are required to suppress the accelerated nonsense-mediated mRNA decay (NMD), to correct the CFTR conformational defect caused by misincorporated amino acids, and to enhance the inefficient stop codon readthrough. The G418-induced readthrough outcome was previously investigated only in reporter models that mimic the impact of the local sequence context on PTC mutations in CFTR. To identify the misincorporated amino acids and their ratios for PTCs in the context of full-length CFTR readthrough, we developed an affinity purification (AP)-tandem mass spectrometry (AP-MS/MS) pipeline. We confirmed the incorporation of Cys, Arg, and Trp residues at the UGA stop codons of G542X, R1162X, and S1196X in CFTR. Notably, we observed that the Cys and Arg incorporation was favored over that of Trp into these CFTR PTCs, suggesting that the transcript sequence beyond the proximity of PTCs and/or other factors can impact the amino acid incorporation and full-length CFTR functional expression. Additionally, establishing the misincorporated amino acid ratios in the readthrough CFTR PTCs aided in maximizing the functional rescue efficiency of PTCs by optimizing CFTR modulator combinations. Collectively, our findings contribute to the understanding of molecular defects underlying various CFTR nonsense mutations and provide a foundation to refine mutation-dependent therapeutic strategies for various CF-causing nonsense mutations.
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Affiliation(s)
| | - Ruiji Ming
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Abed Baiad
- Department of Physiology, McGill University, Montréal, QC, Canada
| | | | - Haijin Xu
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Denis Faubert
- IRCM Mass Spectrometry and Proteomics Platform, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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7
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Bharti N, Santos L, Davyt M, Behrmann S, Eichholtz M, Jimenez-Sanchez A, Hong JS, Rab A, Sorscher EJ, Albers S, Ignatova Z. Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations. Nat Commun 2024; 15:2957. [PMID: 38580646 PMCID: PMC10997658 DOI: 10.1038/s41467-024-47258-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
Nonsense mutations - the underlying cause of approximately 11% of all genetic diseases - prematurely terminate protein synthesis by mutating a sense codon to a premature stop or termination codon (PTC). An emerging therapeutic strategy to suppress nonsense defects is to engineer sense-codon decoding tRNAs to readthrough and restore translation at PTCs. However, the readthrough efficiency of the engineered suppressor tRNAs (sup-tRNAs) largely varies in a tissue- and sequence context-dependent manner and has not yet yielded optimal clinical efficacy for many nonsense mutations. Here, we systematically analyze the suppression efficacy at various pathogenic nonsense mutations. We discover that the translation velocity of the sequence upstream of PTCs modulates the sup-tRNA readthrough efficacy. The PTCs most refractory to suppression are embedded in a sequence context translated with an abrupt reversal of the translation speed leading to ribosomal collisions. Moreover, modeling translation velocity using Ribo-seq data can accurately predict the suppression efficacy at PTCs. These results reveal previously unknown molecular signatures contributing to genotype-phenotype relationships and treatment-response heterogeneity, and provide the framework for the development of personalized tRNA-based gene therapies.
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Affiliation(s)
- Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Stine Behrmann
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marie Eichholtz
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | | | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Andras Rab
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
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8
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Gemmati D, D’Aversa E, Antonica B, Grisafi M, Salvatori F, Pizzicotti S, Pellegatti P, Ciccone M, Moratelli S, Serino ML, Tisato V. Gene Dosage of F5 c.3481C>T Stop-Codon (p.R1161Ter) Switches the Clinical Phenotype from Severe Thrombosis to Recurrent Haemorrhage: Novel Hypotheses for Readthrough Strategy. Genes (Basel) 2024; 15:432. [PMID: 38674367 PMCID: PMC11050146 DOI: 10.3390/genes15040432] [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: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Inherited defects in the genes of blood coagulation essentially express the severity of the clinical phenotype that is directly correlated to the number of mutated alleles of the candidate leader gene (e.g., heterozygote vs. homozygote) and of possible additional coinherited traits. The F5 gene, which codes for coagulation factor V (FV), plays a two-faced role in the coagulation cascade, exhibiting both procoagulant and anticoagulant functions. Thus, defects in this gene can be predisposed to either bleeding or thrombosis. A Sanger sequence analysis detected a premature stop-codon in exon 13 of the F5 gene (c.3481C>T; p.R1161Ter) in several members of a family characterised by low circulating FV levels and contrasting clinical phenotypes. The propositus, a 29 y.o. male affected by recurrent haemorrhages, was homozygous for the F5 stop-codon and for the F5 c.1691G>A (p.R506Q; FV-Leiden) inherited from the heterozygous parents, which is suggestive of combined cis-segregation. The homozygous condition of the stop-codon completely abolished the F5 gene expression in the propositus (FV:Ag < 1%; FV:C < 1%; assessed by ELISA and PT-based one-stage clotting assay respectively), removing, in turn, any chance for FV-Leiden to act as a prothrombotic molecule. His father (57 y.o.), characterised by severe recurrent venous thromboses, underwent a complete molecular thrombophilic screening, revealing a heterozygous F2 G20210A defect, while his mother (56 y.o.), who was negative for further common coagulation defects, reported fully asymptomatic anamnesis. To dissect these conflicting phenotypes, we performed the ProC®Global (Siemens Helthineers) coagulation test aimed at assessing the global pro- and anticoagulant balance of each family member, investigating the responses to the activated protein C (APC) by means of an APC-sensitivity ratio (APC-sr). The propositus had an unexpectedly poor response to APC (APC-sr: 1.09; n.v. > 2.25), and his father and mother had an APC-sr of 1.5 and 2.0, respectively. Although ProC®Global prevalently detects the anticoagulant side of FV, the exceptionally low APC-sr of the propositus and his discordant severe-moderate haemorrhagic phenotype could suggest a residual expression of mutated FV p.506QQ through a natural readthrough or possible alternative splicing mechanisms. The coagulation pathway may be physiologically rebalanced through natural and induced strategies, and the described insights might be able to track the design of novel treatment approaches and rebalancing molecules.
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Affiliation(s)
- Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- University Strategic Centre for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Elisabetta D’Aversa
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Bianca Antonica
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Miriana Grisafi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Francesca Salvatori
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | | | | | - Maria Ciccone
- Haematology Unit, Hospital-University of Ferrara, 44121 Ferrara, Italy
| | - Stefano Moratelli
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Luisa Serino
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Veronica Tisato
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- University Strategic Centre for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory of Technology for Advanced Therapies (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy
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9
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Mangkalaphiban K, Fu L, Du M, Thrasher K, Keeling KM, Bedwell DM, Jacobson A. Extended stop codon context predicts nonsense codon readthrough efficiency in human cells. Nat Commun 2024; 15:2486. [PMID: 38509072 PMCID: PMC10954755 DOI: 10.1038/s41467-024-46703-z] [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: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Protein synthesis terminates when a stop codon enters the ribosome's A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. Seeking to understand readthrough regulation we used a machine learning approach to analyze readthrough efficiency data from published HEK293T ribosome profiling experiments and compared it to comparable yeast experiments. We obtained evidence for the conservation of identities of the stop codon, its context, and 3'-UTR length (when termination is compromised), but not the P-site codon, suggesting a P-site tRNA role in readthrough regulation. Models trained on data from cells treated with the readthrough-promoting drug, G418, accurately predicted readthrough of premature termination codons arising from CFTR nonsense alleles that cause cystic fibrosis. This predictive ability has the potential to aid development of nonsense suppression therapies by predicting a patient's likelihood of improvement in response to drugs given their nonsense mutation sequence context.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
- Department of Genomics and Computational Biology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ming Du
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
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10
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Xiao L, Sun H, Cheng R, Yang R, Jin X, Xu Z, Cai Y, Yang Y, Pang F, Xue G, Wang P, Jiang Q, Nie H. Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102129. [PMID: 38370981 PMCID: PMC10869908 DOI: 10.1016/j.omtn.2024.102129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis. We classified definitive tumor and normal epithelial cells via genetic aberrations and demonstrated dynamic changes in the epithelial-mesenchymal continuum in both epithelial cancer cells and CTCs. We provide the landscape of alternative splicing in CTCs at different stages of EMT, uncovering cell-type-specific splicing patterns and splicing events in cell surface proteins suitable for therapies. We show that MBNL1 governs cell fate through alternative splicing independently of changes in gene expression and affects the splicing pattern during EMT. We found a high frequency of events that contained multiple premature termination codons and were enriched with C and G nucleotides in close proximity, which influence the likelihood of stop codon readthrough and expand the range of potential therapeutic targets. Our study provides insights into the EMT transcriptome's dynamic changes and identifies potential diagnostic and therapeutic targets in pancreatic cancer.
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Affiliation(s)
- Lixing Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Haoxiu Sun
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Rongrong Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Zhaochun Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yideng Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yuexin Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Fenglan Pang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Pingping Wang
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
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11
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Krueger J, Preusse M, Oswaldo Gomez N, Frommeyer YN, Doberenz S, Lorenz A, Kordes A, Grobe S, Müsken M, Depledge DP, Svensson SL, Weiss S, Kaever V, Pich A, Sharma CM, Ignatova Z, Häussler S. tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2312874121. [PMID: 38451943 PMCID: PMC10945773 DOI: 10.1073/pnas.2312874121] [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: 07/28/2023] [Accepted: 12/29/2023] [Indexed: 03/09/2024] Open
Abstract
The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche.
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Affiliation(s)
- Jonas Krueger
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Yannick Noah Frommeyer
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Sebastian Doberenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Anne Lorenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Adrian Kordes
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
| | - Svenja Grobe
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig38124, Germany
| | - Daniel P. Depledge
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Institute of Virology, Hannover Medical School, Hannover30625, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover30625, Germany
| | - Sarah L. Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover, Hannover30625, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Andreas Pich
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Cynthia M. Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University Hamburg, 20146, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital—Rigshospitalet, Copenhagen2100, Denmark
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12
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Zandanell J, Wießner M, Bauer JW, Wagner RN. Stop codon readthrough as a treatment option for epidermolysis bullosa-Where we are and where we are going. Exp Dermatol 2024; 33:e15042. [PMID: 38459626 DOI: 10.1111/exd.15042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024]
Abstract
In the context of rare genetic diseases caused by nonsense mutations, the concept of induced stop codon readthrough (SCR) represents an attractive avenue in the ongoing search for improved treatment options. Epidermolysis bullosa (EB)-exemplary for this group of diseases-describes a diverse group of rare, blistering genodermatoses. Characterized by extreme skin fragility upon minor mechanical trauma, the most severe forms often result from nonsense mutations that lead to premature translation termination and loss of function of essential proteins at the dermo-epidermal junction. Since no curative interventions are currently available, medical care is mainly limited to alleviating symptoms and preventing complications. Complementary to attempts of gene, cell and protein therapy in EB, SCR represents a promising medical alternative. While gentamicin has already been examined in several clinical trials involving EB, other potent SCR inducers, such as ataluren, may also show promise in treating the hitherto non-curative disease. In addition to the extensively studied aminoglycosides and their derivatives, several other substance classes-non-aminoglycoside antibiotics and non-aminoglycoside compounds-are currently under investigation. The extensive data gathered in numerous in vitro experiments and the perspectives they reveal in the clinical setting will be discussed in this review.
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Affiliation(s)
- Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Johann W Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Roland N Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
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13
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Takallou S, Hajikarimlou M, Al-Gafari M, Wang J, Kazmirchuk TDD, Said KB, Samanfar B, Golshani A. The Involvement of YNR069C in Protein Synthesis in the Baker's Yeast, Saccharomyces cerevisiae. BIOLOGY 2024; 13:138. [PMID: 38534408 DOI: 10.3390/biology13030138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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14
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Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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15
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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16
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Khandia R, Gurjar P, Kamal MA, Greig NH. Relative synonymous codon usage and codon pair analysis of depression associated genes. Sci Rep 2024; 14:3502. [PMID: 38346990 PMCID: PMC10861588 DOI: 10.1038/s41598-024-51909-8] [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: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, MP, India.
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamilnadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Mohammad Amjad Kamal
- Joint Laboratory of Artificial Intelligence in Healthcare, Institutes for Systems Genetics and West China School of Nursing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee place, Hebersham, NSW, 2770, Australia
| | - Nigel H Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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17
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Huang ME, Qin Y, Shang Y, Hao Q, Zhan C, Lian C, Luo S, Liu LD, Zhang S, Zhang Y, Wo Y, Li N, Wu S, Gui T, Wang B, Luo Y, Cai Y, Liu X, Xu Z, Dai P, Li S, Zhang L, Dong J, Wang J, Zheng X, Xu Y, Sun Y, Wu W, Yeap LS, Meng FL. C-to-G editing generates double-strand breaks causing deletion, transversion and translocation. Nat Cell Biol 2024; 26:294-304. [PMID: 38263276 DOI: 10.1038/s41556-023-01342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
Base editors (BEs) introduce base substitutions without double-strand DNA cleavage. Besides precise substitutions, BEs generate low-frequency 'stochastic' byproducts through unclear mechanisms. Here, we performed in-depth outcome profiling and genetic dissection, revealing that C-to-G BEs (CGBEs) generate substantial amounts of intermediate double-strand breaks (DSBs), which are at the centre of several byproducts. Imperfect DSB end-joining leads to small deletions via end-resection, templated insertions or aberrant transversions during end fill-in. Chromosomal translocations were detected between the editing target and off-targets of Cas9/deaminase origin. Genetic screenings of DNA repair factors disclosed a central role of abasic site processing in DSB formation. Shielding of abasic sites by the suicide enzyme HMCES reduced CGBE-initiated DSBs, providing an effective way to minimize DSB-triggered events without affecting substitutions. This work demonstrates that CGBEs can initiate deleterious intermediate DSBs and therefore require careful consideration for therapeutic applications, and that HMCES-aided CGBEs hold promise as safer tools.
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Affiliation(s)
- Min Emma Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yining Qin
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yafang Shang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Qian Hao
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanzong Zhan
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoyang Lian
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Simin Luo
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Daisy Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Wo
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuheng Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Tuantuan Gui
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binbin Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifeng Luo
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yanni Cai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Ziye Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Pengfei Dai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Simiao Li
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Junchao Dong
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihua Sun
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Leng-Siew Yeap
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China.
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18
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Coller J, Ignatova Z. tRNA therapeutics for genetic diseases. Nat Rev Drug Discov 2024; 23:108-125. [PMID: 38049504 DOI: 10.1038/s41573-023-00829-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2023] [Indexed: 12/06/2023]
Abstract
Transfer RNAs (tRNAs) have a crucial role in protein synthesis, and in recent years, their therapeutic potential for the treatment of genetic diseases - primarily those associated with a mutation altering mRNA translation - has gained significant attention. Engineering tRNAs to readthrough nonsense mutation-associated premature termination of mRNA translation can restore protein synthesis and function. In addition, supplementation of natural tRNAs can counteract effects of missense mutations in proteins crucial for tRNA biogenesis and function in translation. This Review will present advances in the development of tRNA therapeutics with high activity and safety in vivo and discuss different formulation approaches for single or chronic treatment modalities. The field of tRNA therapeutics is still in its early stages, and a series of challenges related to tRNA efficacy and stability in vivo, delivery systems with tissue-specific tropism, and safe and efficient manufacturing need to be addressed.
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Affiliation(s)
- Jeff Coller
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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19
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Salpietro V, Maroofian R, Zaki MS, Wangen J, Ciolfi A, Barresi S, Efthymiou S, Lamaze A, Aughey GN, Al Mutairi F, Rad A, Rocca C, Calì E, Accogli A, Zara F, Striano P, Mojarrad M, Tariq H, Giacopuzzi E, Taylor JC, Oprea G, Skrahina V, Rehman KU, Abd Elmaksoud M, Bassiony M, El Said HG, Abdel-Hamid MS, Al Shalan M, Seo G, Kim S, Lee H, Khang R, Issa MY, Elbendary HM, Rafat K, Marinakis NM, Traeger-Synodinos J, Ververi A, Sourmpi M, Eslahi A, Khadivi Zand F, Beiraghi Toosi M, Babaei M, Jackson A, Bertoli-Avella A, Pagnamenta AT, Niceta M, Battini R, Corsello A, Leoni C, Chiarelli F, Dallapiccola B, Faqeih EA, Tallur KK, Alfadhel M, Alobeid E, Maddirevula S, Mankad K, Banka S, Ghayoor-Karimiani E, Tartaglia M, Chung WK, Green R, Alkuraya FS, Jepson JEC, Houlden H. Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome. Am J Hum Genet 2024; 111:200-210. [PMID: 38118446 PMCID: PMC10806450 DOI: 10.1016/j.ajhg.2023.11.012] [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: 05/15/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Jamie Wangen
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Sabina Barresi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Angelique Lamaze
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK; Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Gabriel N Aughey
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Fuad Al Mutairi
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Elisa Calì
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Andrea Accogli
- Division of Medical Genetics, Department of Pediatrics, McGill University, Montreal, Canada
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Unit of Pediatric Neurology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Huma Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Edoardo Giacopuzzi
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Genomics Research Centre, Human Technopole, Milan, Italy; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Mahmoud Bassiony
- Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Huda G El Said
- Department of Family Health, High Institute of Public Health, University of Alexandria, Alexandria, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha Al Shalan
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | | | - Mahmoud Y Issa
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina Ververi
- Genetics Unit, Department of Obstetrics & Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Thessaloniki, Greece
| | | | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran
| | | | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Antonio Corsello
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Women and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | | | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Eissa Ali Faqeih
- Unit of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Majid Alfadhel
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital, London, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Ehsan Ghayoor-Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, University of London, St George's, Cranmer Terrace, London SW17 0RE, UK
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - James E C Jepson
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
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20
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Wimmer B, Friedrich A, Poeltner K, Edobor G, Mosshammer C, Temaj G, Rathner A, Karl T, Krauss J, von Hagen J, Gerner C, Breitenbach M, Hintner H, Bauer JW, Breitenbach-Koller H. En Route to Targeted Ribosome Editing to Replenish Skin Anchor Protein LAMB3 in Junctional Epidermolysis Bullosa. JID INNOVATIONS 2024; 4:100240. [PMID: 38282649 PMCID: PMC10810840 DOI: 10.1016/j.xjidi.2023.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024] Open
Abstract
Severe junctional epidermolysis bullosa is a rare genetic, postpartum lethal skin disease, predominantly caused by nonsense/premature termination codon (PTC) sequence variants in LAMB3 gene. LAMB3 encodes LAMB3, the β subunit of epidermal-dermal skin anchor laminin 332. Most translational reads of a PTC mRNA deliver truncated, nonfunctional proteins, whereas an endogenous PTC readthrough mechanism produces full-length protein at minimal and insufficient levels. Conventional translational readthrough-inducing drugs amplify endogenous PTC readthrough; however, translational readthrough-inducing drugs are either proteotoxic or nonselective. Ribosome editing is a more selective and less toxic strategy. This technique identified ribosomal protein L35/uL29 (ie, RpL35) and RpL35-ligands repurposable drugs artesunate and atazanavir as molecular tools to increase production levels of full-length LAMB3. To evaluate ligand activity in living cells, we monitored artesunate and atazanavir treatment by dual luciferase reporter assays. Production levels of full-length LAMB3 increased up to 200% upon artesunate treatment, up to 150% upon atazanavir treatment, and up to 170% upon combinatorial treatment of RpL35 ligands at reduced drug dosage, with an unrelated PTC reporter being nonresponsive. Proof of bioactivity of RpL35 ligands in selective increase of full-length LAMB3 provides the basis for an alternative, targeted therapeutic route to replenish LAMB3 in severe junctional epidermolysis bullosa.
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Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Claudia Mosshammer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University of Linz, Linz, Austria
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Jan Krauss
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- SKM-IP PartGmbB, Munich, Germany
| | - Joerg von Hagen
- Merck KGaA, Gernsheim, Germany
- ryon-Greentech Accelerator, Gernsheim, Germany
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
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21
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Khandia R, Gurjar P, Romashchenko V, Al-Hussain SA, Alexiou A, Zouganelis G, Zaki MEA. In-silico Codon Context and Synonymous Usage Analysis of Genes for Molecular Mechanisms Inducing Autophagy and Apoptosis with Reference to Neurodegenerative Disorders. J Alzheimers Dis 2024; 99:927-939. [PMID: 38728191 DOI: 10.3233/jad-240158] [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] [Indexed: 05/12/2024]
Abstract
Background Autophagy and apoptosis are cellular processes that maintain cellular homeostasis and remove damaged or aged organelles or aggregated and misfolded proteins. Stress factors initiate the signaling pathways common to autophagy and apoptosis. An imbalance in the autophagy and apoptosis, led by cascade of molecular mechanism prior to both processes culminate into neurodegeneration. Objective In present study, we urge to investigate the codon usage pattern of genes which are common before initiating autophagy and apoptosis. Methods In the present study, we took up eleven genes (DAPK1, BECN1, PIK3C3 (VPS34), BCL2, MAPK8, BNIP3 L (NIX), PMAIP1, BAD, BID, BBC3, MCL1) that are part of molecular signaling mechanism prior to autophagy and apoptosis. We analyzed dinucleotide odds ratio, codon bias, usage, context, and rare codon analysis. Results CpC and GpG dinucleotides were abundant, with the dominance of G/C ending codons as preferred codons. Clustering analysis revealed that MAPK8 had a distinct codon usage pattern compared to other envisaged genes. Both positive and negative contexts were observed, and GAG-GAG followed by CTG-GCC was the most abundant codon pair. Of the six synonymous arginine codons, two codons CGT and CGA were the rarest. Conclusions The information presented in the study may be used to manipulate the process of autophagy and apoptosis and to check the pathophysiology associated with their dysregulation.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, NSW, Australia
| | | | - Sami A Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, NSW, Australia
- University Centre for Research & Development, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
- Department of Research & Development, Funogen, Athens, Greece
- Department of Research & Development, AFNP Med, Wienna, Austria
| | - George Zouganelis
- School of Human Sciences, College of Life and Natural Sciences, University of Derby, Kedleston Road, Derby, UK
| | - Magdi E A Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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22
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Blomquist VG, Niu J, Choudhury P, Al Saneh A, Colecraft HM, Ahern CA. Transfer RNA-mediated restoration of potassium current and electrical correction in premature termination long-QT syndrome hERG mutants. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102032. [PMID: 37842167 PMCID: PMC10568093 DOI: 10.1016/j.omtn.2023.102032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Disease-causing premature termination codons (PTCs) individually disrupt the functional expression of hundreds of genes and represent a pernicious clinical challenge. In the heart, loss-of-function mutations in the hERG potassium channel account for approximately 30% of long-QT syndrome arrhythmia, a lethal cardiac disorder with limited treatment options. Premature termination of ribosomal translation produces a truncated and, for potassium channels, a potentially dominant-negative protein that impairs the functional assembly of the wild-type homotetrameric hERG channel complex. We used high-throughput flow cytometry and patch-clamp electrophysiology to assess the trafficking and voltage-dependent activity of hERG channels carrying patient PTC variants that have been corrected by anticodon engineered tRNA. Adenoviral-mediated expression of mutant hERG channels in cultured adult guinea pig cardiomyocytes prolonged action potential durations, and this deleterious effect was corrected upon adenoviral delivery of a human ArgUGA tRNA to restore full-length hERG protein. The results demonstrate mutation-specific, context-agnostic PTC correction and elevate the therapeutic potential of this approach for rare genetic diseases caused by stop codons.
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Affiliation(s)
- Viggo G. Blomquist
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacqueline Niu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Papiya Choudhury
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ahmad Al Saneh
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Henry M. Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Christopher A. Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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23
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Wittenstein A, Caspi M, Rippin I, Elroy-Stein O, Eldar-Finkelman H, Thoms S, Rosin-Arbesfeld R. Nonsense mutation suppression is enhanced by targeting different stages of the protein synthesis process. PLoS Biol 2023; 21:e3002355. [PMID: 37943958 PMCID: PMC10684085 DOI: 10.1371/journal.pbio.3002355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023] Open
Abstract
The introduction of premature termination codons (PTCs), as a result of splicing defects, insertions, deletions, or point mutations (also termed nonsense mutations), lead to numerous genetic diseases, ranging from rare neuro-metabolic disorders to relatively common inheritable cancer syndromes and muscular dystrophies. Over the years, a large number of studies have demonstrated that certain antibiotics and other synthetic molecules can act as PTC suppressors by inducing readthrough of nonsense mutations, thereby restoring the expression of full-length proteins. Unfortunately, most PTC readthrough-inducing agents are toxic, have limited effects, and cannot be used for therapeutic purposes. Thus, further efforts are required to improve the clinical outcome of nonsense mutation suppressors. Here, by focusing on enhancing readthrough of pathogenic nonsense mutations in the adenomatous polyposis coli (APC) tumor suppressor gene, we show that disturbing the protein translation initiation complex, as well as targeting other stages of the protein translation machinery, enhances both antibiotic and non-antibiotic-mediated readthrough of nonsense mutations. These findings strongly increase our understanding of the mechanisms involved in nonsense mutation readthrough and facilitate the development of novel therapeutic targets for nonsense suppression to restore protein expression from a large variety of disease-causing mutated transcripts.
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Affiliation(s)
- Amnon Wittenstein
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Rippin
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Eldar-Finkelman
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sven Thoms
- Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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24
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Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J. Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res 2023; 51:10606-10618. [PMID: 37742077 PMCID: PMC10602869 DOI: 10.1093/nar/gkad778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study, we report that combined aminoacylation and editing defects cause severe proteotoxicity. We show that the ths1-C268A mutation in yeast threonyl-tRNA synthetase (ThrRS) abolishes editing and causes heat sensitivity. Surprisingly, experimental evolution of the mutant results in intragenic mutations that restore heat resistance but not editing. ths1-C268A destabilizes ThrRS and decreases overall Thr-tRNAThr synthesis, while the suppressor mutations in the evolved strains improve aminoacylation. We further show that deficiency in either ThrRS aminoacylation or editing is insufficient to cause heat sensitivity, and that ths1-C268A impairs ribosome-associated quality control. Our results suggest that aminoacylation deficiency predisposes cells to proteotoxic stress.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jason Yu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Sukyeong Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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25
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Liu Z, Wang J, Shi Y, Yee BA, Terrey M, Zhang Q, Lee JC, Lin KI, Wang AHJ, Ackerman S, Yeo G, Cui H, Yang XL. Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. Nucleic Acids Res 2023; 51:10768-10781. [PMID: 37739431 PMCID: PMC10602924 DOI: 10.1093/nar/gkad773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/17/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). Here we found that components of the human selenocysteine incorporation machinery (SerRS, tRNASec, and eEFSec) also increased translational readthrough of non-selenocysteine genes, including VEGFA, to create C-terminally extended isoforms. SerRS recognizes target mRNAs through a stem-loop structure that resembles the variable loop of its cognate tRNAs. This function of SerRS depends on both its enzymatic activity and a vertebrate-specific domain. Through eCLIP-seq, we identified additional SerRS-interacting mRNAs as potential readthrough genes. Moreover, SerRS overexpression was sufficient to reverse premature termination caused by a pathogenic nonsense mutation. Our findings expand the repertoire of selenoprotein biosynthesis machinery and suggest an avenue for therapeutic targeting of nonsense mutations using endogenous factors.
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Affiliation(s)
- Ze Liu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Justin Wang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yi Shi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Biochemistry, School of Medicine, Nankai University, Tianjin, China
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Qian Zhang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jenq-Chang Lee
- Department of Surgery, National Cheng Kung University Medical College and Hospital, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taiwan
| | - Andrew H-J Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Neurobiology, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Haissi Cui
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Perriera R, Vitale E, Pibiri I, Carollo PS, Ricci D, Corrao F, Fiduccia I, Melfi R, Zizzo MG, Tutone M, Pace A, Lentini L. Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression. Int J Mol Sci 2023; 24:15084. [PMID: 37894764 PMCID: PMC10606485 DOI: 10.3390/ijms242015084] [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: 08/11/2023] [Revised: 09/11/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.
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Affiliation(s)
| | | | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
| | | | | | | | | | | | | | | | | | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
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27
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Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F, Schirle M, Couttet P, Sigoillot F, Ziegelmüller J, Uldry AC, Teodorowicz W, Schmiedeberg N, Mühlemann O, Reinhardt J. Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep 2023; 42:113056. [PMID: 37651229 DOI: 10.1016/j.celrep.2023.113056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Suppression of premature termination codons (PTCs) by translational readthrough is a promising strategy to treat a wide variety of severe genetic diseases caused by nonsense mutations. Here, we present two potent readthrough promoters-NVS1.1 and NVS2.1-that restore substantial levels of functional full-length CFTR and IDUA proteins in disease models for cystic fibrosis and Hurler syndrome, respectively. In contrast to other readthrough promoters that affect stop codon decoding, the NVS compounds stimulate PTC suppression by triggering rapid proteasomal degradation of the translation termination factor eRF1. Our results show that this occurs by trapping eRF1 in the terminating ribosome, causing ribosome stalls and subsequent ribosome collisions, and activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25.
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Affiliation(s)
- Lukas-Adrian Gurzeler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marion Link
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Yvonne Ibig
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Olaf Galuba
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | | | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Francis Bitsch
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Philipp Couttet
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Jana Ziegelmüller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Wojciech Teodorowicz
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Jürgen Reinhardt
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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28
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Wong KM, Wegener E, Baradaran-Heravi A, Huppke B, Gärtner J, Huppke P. Evaluation of Novel Enhancer Compounds in Gentamicin-Mediated Readthrough of Nonsense Mutations in Rett Syndrome. Int J Mol Sci 2023; 24:11665. [PMID: 37511424 PMCID: PMC10380790 DOI: 10.3390/ijms241411665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Rett syndrome (RTT), a severe X-linked neurodevelopmental disorder, is primarily caused by mutations in the methyl CpG binding protein 2 gene (MECP2). Over 35% RTT patients carry nonsense mutation in MECP2, making it a suitable candidate disease for nonsense suppression therapy. In our previous study, gentamicin was found to induce readthrough of MECP2 nonsense mutations with modest efficiency. Given the recent discovery of readthrough enhancers, CDX compounds, we herein evaluated the potentiation effect of CDX5-1, CDX5-288, and CDX6-180 on gentamicin-mediated readthrough efficiency in transfected HeLa cell lines bearing the four most common MECP2 nonsense mutations. We showed that all three CDX compounds potentiated gentamicin-mediated readthrough and increased full-length MeCP2 protein levels in cells expressing the R168X, R255X, R270X, and R294X nonsense mutations. Among all three CDX compounds, CDX5-288 was the most potent enhancer and enabled the use of reduced doses of gentamicin, thus mitigating the toxicity. Furthermore, we successfully demonstrated the upregulation of full-length Mecp2 protein expression in fibroblasts derived from Mecp2R255X/Y mice through combinatorial treatment. Taken together, findings demonstrate the feasibility of this combinatorial approach to nonsense suppression therapy for a subset of RTT patients.
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Affiliation(s)
- Keit Men Wong
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Eike Wegener
- Department of Pediatrics and Adolescent Medicine, Division of Neuropediatrics, Pediatric Neurology University Medical Center Göttingen, Georg August University Göttingen, 37075 Göttingen, Germany
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Brenda Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, Division of Neuropediatrics, Pediatric Neurology University Medical Center Göttingen, Georg August University Göttingen, 37075 Göttingen, Germany
| | - Peter Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
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29
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Li S, Li J, Shi W, Nie Z, Zhang S, Ma F, Hu J, Chen J, Li P, Xie X. Pharmaceuticals Promoting Premature Termination Codon Readthrough: Progress in Development. Biomolecules 2023; 13:988. [PMID: 37371567 DOI: 10.3390/biom13060988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Around 11% of all known gene lesions causing human genetic diseases are nonsense mutations that introduce a premature stop codon (PTC) into the protein-coding gene sequence. Drug-induced PTC readthrough is a promising therapeutic strategy for treating hereditary diseases caused by nonsense mutations. To date, it has been found that more than 50 small-molecular compounds can promote PTC readthrough, known as translational readthrough-inducing drugs (TRIDs), and can be divided into two major categories: aminoglycosides and non-aminoglycosides. This review summarizes the pharmacodynamics and clinical application potential of the main TRIDs discovered so far, especially some newly discovered TRIDs in the past decade. The discovery of these TRIDs brings hope for treating nonsense mutations in various genetic diseases. Further research is still needed to deeply understand the mechanism of eukaryotic cell termination and drug-induced PTC readthrough so that patients can achieve the greatest benefit from the various TRID treatments.
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Affiliation(s)
- Shan Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Juan Li
- Central Laboratory, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Genetic Study of Hematopathy, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wenjing Shi
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ziyan Nie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shasha Zhang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fengdie Ma
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jun Hu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jianjun Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Peiqiang Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
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30
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Müller MBD, Kasturi P, Jayaraj GG, Hartl FU. Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control. Cell 2023:S0092-8674(23)00587-1. [PMID: 37339632 PMCID: PMC10364623 DOI: 10.1016/j.cell.2023.05.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023]
Abstract
Readthrough into the 3' untranslated region (3' UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in Caenorhabditis elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome-collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions (CTEs) are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes collide at nonoptimal codons, enriched in 3' UTRs, transmembrane proteins, and collagens. GCN1 dysfunction increasingly perturbs these protein classes during aging, resulting in mRNA and proteome imbalance. Our results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.
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Affiliation(s)
- Martin B D Müller
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Prasad Kasturi
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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31
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Albers S, Allen EC, Bharti N, Davyt M, Joshi D, Perez-Garcia CG, Santos L, Mukthavaram R, Delgado-Toscano MA, Molina B, Kuakini K, Alayyoubi M, Park KJJ, Acharya G, Gonzalez JA, Sagi A, Birket SE, Tearney GJ, Rowe SM, Manfredi C, Hong JS, Tachikawa K, Karmali P, Matsuda D, Sorscher EJ, Chivukula P, Ignatova Z. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 2023; 618:842-848. [PMID: 37258671 PMCID: PMC10284701 DOI: 10.1038/s41586-023-06133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
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Affiliation(s)
- Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | | | | | | | | | | | | | - Amit Sagi
- Arcturus Therapeutics, San Diego, CA, USA
| | - Susan E Birket
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MA, Cambridge, USA
| | - Steven M Rowe
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candela Manfredi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | | | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | | | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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32
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Russell PJ, Slivka JA, Boyle EP, Burghes AHM, Kearse MG. Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay. RNA (NEW YORK, N.Y.) 2023; 29:735-744. [PMID: 36878710 PMCID: PMC10187673 DOI: 10.1261/rna.079525.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/14/2023] [Indexed: 05/18/2023]
Abstract
It is estimated that nearly 50% of mammalian transcripts contain at least one upstream open reading frame (uORF), which are typically one to two orders of magnitude smaller than the downstream main ORF. Most uORFs are thought to be inhibitory as they sequester the scanning ribosome, but in some cases allow for translation reinitiation. However, termination in the 5' UTR at the end of uORFs resembles premature termination that is normally sensed by the nonsense-mediated mRNA decay (NMD) pathway. Translation reinitiation has been proposed as a method for mRNAs to prevent NMD. Here, we test how uORF length influences translation reinitiation and mRNA stability in HeLa cells. Using custom 5' UTRs and uORF sequences, we show that reinitiation can occur on heterologous mRNA sequences, favors small uORFs, and is supported when initiation occurs with more initiation factors. After determining reporter mRNA half-lives in HeLa cells and mining available mRNA half-life data sets for cumulative predicted uORF length, we conclude that translation reinitiation after uORFs is not a robust method for mRNAs to prevent NMD. Together, these data suggest that the decision of whether NMD ensues after translating uORFs occurs before reinitiation in mammalian cells.
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Affiliation(s)
- Paul J Russell
- Cellular, Molecular, and Biochemical Sciences Program, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jacob A Slivka
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaina P Boyle
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael G Kearse
- Cellular, Molecular, and Biochemical Sciences Program, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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33
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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.
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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.
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34
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Kesner JS, Chen Z, Shi P, Aparicio AO, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X. Noncoding translation mitigation. Nature 2023; 617:395-402. [PMID: 37046090 PMCID: PMC10560126 DOI: 10.1038/s41586-023-05946-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/13/2023] [Indexed: 04/14/2023]
Abstract
Translation is pervasive outside of canonical coding regions, occurring in long noncoding RNAs, canonical untranslated regions and introns1-4, especially in ageing4-6, neurodegeneration5,7 and cancer8-10. Notably, the majority of tumour-specific antigens are results of noncoding translation11-13. Although the resulting polypeptides are often nonfunctional, translation of noncoding regions is nonetheless necessary for the birth of new coding sequences14,15. The mechanisms underlying the surveillance of translation in diverse noncoding regions and how escaped polypeptides evolve new functions remain unclear10,16-19. Functional polypeptides derived from annotated noncoding sequences often localize to membranes20,21. Here we integrate massively parallel analyses of more than 10,000 human genomic sequences and millions of random sequences with genome-wide CRISPR screens, accompanied by in-depth genetic and biochemical characterizations. Our results show that the intrinsic nucleotide bias in the noncoding genome and in the genetic code frequently results in polypeptides with a hydrophobic C-terminal tail, which is captured by the ribosome-associated BAG6 membrane protein triage complex for either proteasomal degradation or membrane targeting. By contrast, canonical proteins have evolved to deplete C-terminal hydrophobic residues. Our results reveal a fail-safe mechanism for the surveillance of unwanted translation from diverse noncoding regions and suggest a possible biochemical route for the preferential membrane localization of newly evolved proteins.
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Affiliation(s)
- Jordan S Kesner
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ziheng Chen
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Peiguo Shi
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexis O Aparicio
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael R Murphy
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yang Guo
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aditi Trehan
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica E Lipponen
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yocelyn Recinos
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natura Myeku
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xuebing Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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35
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Zhang N, Zheng W, Bakker W, van Ravenzwaay B, Rietjens IMCM. In vitro models to measure effects on intestinal deconjugation and transport of mixtures of bile acids. Chem Biol Interact 2023; 375:110445. [PMID: 36889625 DOI: 10.1016/j.cbi.2023.110445] [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: 01/10/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023]
Abstract
Bile acid metabolism and transport are critical to maintain bile acid homeostasis and host health. In this study, it was investigated if effects on intestinal bile acid deconjugation and transport can be quantified in vitro model systems using mixtures of bile acids instead of studying individual bile acids. To this end deconjugation of mixtures of selected bile acids in anaerobic rat or human fecal incubations and the effect of the antibiotic tobramycin on these reactions was studied. In addition, the effect of tobramycin on the transport of the bile acids in isolation or in a mixture across Caco-2 cell layers was characterized. The results demonstrate that both the reduction of bile acid deconjugation and transport by tobramycin can be adequately detected in vitro systems using a mixture of bile acids, thus eliminating the need to characterize the effects for each bile acid in separate experiments. Subtle differences between the experiments with single or combined bile acids point at mutual competitive interactions and indicate that the use of bile acid mixtures is preferred over use of single bile acid given that also in vivo bile acids occurs in mixtures.
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Affiliation(s)
- Nina Zhang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708, WE Wageningen, the Netherlands.
| | - Weijia Zheng
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708, WE Wageningen, the Netherlands
| | - Wouter Bakker
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708, WE Wageningen, the Netherlands
| | - Bennard van Ravenzwaay
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708, WE Wageningen, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708, WE Wageningen, the Netherlands
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36
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Wagner RN, Wießner M, Friedrich A, Zandanell J, Breitenbach-Koller H, Bauer JW. Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond. Int J Mol Sci 2023; 24:6101. [PMID: 37047074 PMCID: PMC10093890 DOI: 10.3390/ijms24076101] [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: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.
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Affiliation(s)
- Roland N. Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Andreas Friedrich
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
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37
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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38
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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39
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Adachi H, Pan Y, He X, Chen JL, Klein B, Platenburg G, Morais P, Boutz P, Yu YT. Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes. Mol Cell 2023; 83:637-651.e9. [PMID: 36764303 PMCID: PMC9975048 DOI: 10.1016/j.molcel.2023.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/18/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
Nonsense mutations create premature termination codons (PTCs), activating the nonsense-mediated mRNA decay (NMD) pathway to degrade most PTC-containing mRNAs. The undegraded mRNA is translated, but translation terminates at the PTC, leading to no production of the full-length protein. This work presents targeted PTC pseudouridylation, an approach for nonsense suppression in human cells. Specifically, an artificial box H/ACA guide RNA designed to target the mRNA PTC can suppress both NMD and premature translation termination in various sequence contexts. Targeted pseudouridylation exhibits a level of suppression comparable with that of aminoglycoside antibiotic treatments. When targeted pseudouridylation is combined with antibiotic treatment, a much higher level of suppression is observed. Transfection of a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene targeting the PTC also leads to nonsense suppression. Thus, targeted pseudouridylation is an RNA-directed gene-specific approach that suppresses NMD and concurrently promotes PTC readthrough.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Yi Pan
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Xueyang He
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Bart Klein
- ProQR Therapeutics, Leiden, the Netherlands
| | | | | | - Paul Boutz
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA; Center for Biomedical Informatics and Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.
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40
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Mattheisen JM, Wollowitz JS, Huber T, Sakmar TP. Genetic code expansion to enable site-specific bioorthogonal labeling of functional G protein-coupled receptors in live cells. Protein Sci 2023; 32:e4550. [PMID: 36540928 PMCID: PMC9847076 DOI: 10.1002/pro.4550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
For use in site-specific bioorthogonal labeling of expressed G protein-coupled receptors (GPCRs) in live cells, we developed a luciferase-based reporter assay. The assay was used to compare amber codon suppression efficiency, receptor functionality, and efficiency of different bioorthogonal labeling chemistries. We used the assay system to compare side-by-side the efficiency of incorporation of three different noncanonical amino acids [4-azido-l-phenylalanine (azF), cyclopropene-l-lysine (CpK), and trans-cyclooct-2-en-l-lysine (TCOK)] at three different sites on a GPCR using three different genetic code expansion plasmid systems. As a model GPCR, we engineered an epitope-tagged C-C chemokine receptor 5 (CCR5)-RLuc3 fusion for expression in HEK293T cells. Satisfactory incorporation of azF, CpK, and TCOK into heterologously expressed CCR5 was achieved. We also carried out cell-based calcium mobilization assays to measure the function of the engineered CCR5, and in the same cells, we performed bioorthogonal labeling of the engineered mutants using heterobivalent compounds containing bioorthogonal tethering groups linked to either a small-molecule fluorophore or a peptide. Favorable reaction kinetics of tetrazine-containing compounds with CCR5 harboring TCOK was observed. However, bioorthogonal labeling in live cells of CCR5 harboring CpK with tetrazine-containing compounds using the inverse electron demand Diels-Alder ligation was overall slightly more efficient than other reactions tested.
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Affiliation(s)
- Jordan M. Mattheisen
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
- Tri‐Institutional PhD Program in Chemical BiologyNew YorkNew YorkUSA
| | - Jaina S. Wollowitz
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
- Tri‐Institutional PhD Program in Chemical BiologyNew YorkNew YorkUSA
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal TransductionThe Rockefeller UniversityNew YorkNew YorkUSA
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41
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A High-Throughput Assay for In Vitro Determination of Release Factor-Dependent Peptide Release from a Pretermination Complex by Fluorescence Anisotropy-Application to Nonsense Suppressor Screening and Mechanistic Studies. Biomolecules 2023; 13:biom13020242. [PMID: 36830611 PMCID: PMC9953321 DOI: 10.3390/biom13020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Premature termination codons (PTCs) account for ~12% of all human disease mutations. Translation readthrough-inducing drugs (TRIDs) are prominent among the several therapeutic approaches being used to overcome PTCs. Ataluren is the only TRID that has been approved for treating patients suffering from a PTC disease, Duchenne muscular dystrophy, but it gives variable readthrough results in cells isolated from patients suffering from other PTC diseases. We recently elucidated ataluren's mechanism of action as a competitive inhibitor of release factor complex (RFC) catalysis of premature termination and identified ataluren's binding sites on the ribosome responsible for such an inhibition. These results suggest the possibility of discovering new TRIDs, which would retain ataluren's low toxicity while displaying greater potency and generality in stimulating readthrough via the inhibition of termination. Here we present a detailed description of a new in vitro plate reader assay that we are using both to screen small compound libraries for the inhibition of RFC-dependent peptide release and to better understand the influence of termination codon identity and sequence context on RFC activity.
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42
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Repeat-associated non-AUG translation induces cytoplasmic aggregation of CAG repeat-containing RNAs. Proc Natl Acad Sci U S A 2023; 120:e2215071120. [PMID: 36623192 PMCID: PMC9934169 DOI: 10.1073/pnas.2215071120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
CAG trinucleotide repeat expansions cause several neurodegenerative diseases, including Huntington's disease and spinocerebellar ataxia. RNAs with expanded CAG repeats contribute to disease in two unusual ways. First, these repeat-containing RNAs may agglomerate in the nucleus as foci that sequester several RNA-binding proteins. Second, these RNAs may undergo aberrant repeat-associated non-AUG (RAN) translation in multiple frames and produce aggregation-prone proteins. The relationship between RAN translation and RNA foci, and their relative contributions to cellular dysfunction, are unclear. Here, we show that CAG repeat-containing RNAs that undergo RAN translation first accumulate at nuclear foci and, over time, are exported to the cytoplasm. In the cytoplasm, these RNAs are initially dispersed but, upon RAN translation, aggregate with the RAN translation products. These RNA-RAN protein agglomerates sequester various RNA-binding proteins and are associated with the disruption of nucleocytoplasmic transport and cell death. In contrast, RNA accumulation at nuclear foci alone does not produce discernable defects in nucleocytoplasmic transport or cell viability. Inhibition of RAN translation prevents cytoplasmic RNA aggregation and alleviates cell toxicity. Our findings demonstrate that RAN translation-induced RNA-protein aggregation correlates with the key pathological hallmarks observed in disease and suggest that cytoplasmic RNA aggregation may be an underappreciated phenomenon in CAG trinucleotide repeat expansion disorders.
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43
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Lightfoot HL, Smith GF. Targeting RNA with small molecules-A safety perspective. Br J Pharmacol 2023. [PMID: 36631428 DOI: 10.1111/bph.16027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
RNA is a major player in cellular function, and consequently can drive a number of disease pathologies. Over the past several years, small molecule-RNA targeting (smRNA targeting) has developed into a promising drug discovery approach. Numerous techniques, tools, and assays have been developed to support this field, and significant investments have been made by pharmaceutical and biotechnology companies. To date, the focus has been on identifying disease validated primary targets for smRNA drug development, yet RNA as a secondary (off) target for all small molecule drug programs largely has been unexplored. In this perspective, we discuss structure, target, and mechanism-driven safety aspects of smRNAs and highlight how these parameters can be evaluated in drug discovery programs to produce potentially safer drugs.
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Affiliation(s)
- Helen L Lightfoot
- Safety and Mechanistic Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Graham F Smith
- Data Science and AI, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
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44
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Eisenack TJ, Trentini DB. Ending a bad start: Triggers and mechanisms of co-translational protein degradation. Front Mol Biosci 2023; 9:1089825. [PMID: 36660423 PMCID: PMC9846516 DOI: 10.3389/fmolb.2022.1089825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
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Affiliation(s)
- Tom Joshua Eisenack
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Débora Broch Trentini
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany,*Correspondence: Débora Broch Trentini,
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45
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Beryozkin A, Nagel-Wolfum K, Banin E, Sharon D. Factors Affecting Readthrough of Natural Versus Premature Termination Codons. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:149-155. [PMID: 37440028 DOI: 10.1007/978-3-031-27681-1_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Nonsense mutations occur within the open-reading frame of a gene resulting in a premature termination codon (PTC). PTC-containing mRNAs can either be degeraded or cause premature translation termination producing a truncated protein that can be either nonfunctional or toxic. Translational readthrough inducing drugs (TRIDs) are small molecules that are able to induce readthrough, resulting in the restoration of full-length protein expression. The re-expressed proteins usually harbor a missense change. The effciency of individual TRIDs is variable and varies between different genes and even different nonsense mutations in the same gene. This review summarizes factors, including the sequences located upstream and downstream the disease-causing mutation and the type of PTC, affecting the translational readthrough process by modulating the type of amino acid insertion and the efficiency of the process during readthrough following TRIDs treatments.
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Affiliation(s)
- Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kerstin Nagel-Wolfum
- Institute of Molecular Physiology & Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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46
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Guo R, Yu X, Gregory BD. The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes. PLANT DIRECT 2023; 7:e479. [PMID: 36643787 PMCID: PMC9831718 DOI: 10.1002/pld3.479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
RNA turnover is essential in maintaining messenger RNA (mRNA) homeostasis during various developmental stages and stress responses. Co-translational mRNA decay (CTRD), a process in which mRNAs are degraded while still associated with translating ribosomes, has recently been discovered to function in yeast and three angiosperm transcriptomes. However, it is still unclear how prevalent CTRD across the plant lineage. Moreover, the sequence features of co-translationally decayed mRNAs have not been well-studied. Here, utilizing a collection of publicly available degradome sequencing datasets for another seven angiosperm transcriptomes, we have confirmed that CTRD is functioning in at least 10 angiosperms and likely throughout the plant lineage. Additionally, we have identified sequence features shared by the co-translationally decayed mRNAs in these species, implying a possible conserved triggering mechanism for this pathway. Given that degradome sequencing datasets can also be used to identify actively translating upstream open reading frames (uORFs), which are quite understudied in plants, we have identified numerous actively translating uORFs in the same 10 angiosperms. These findings reveal that actively translating uORFs are prevalent in plant transcriptomes, some of which are conserved across this lineage. We have also observed conserved sequence features in the regions flanking these uORFs' stop codons that might contribute to ribosome stalling at these sequences. Finally, we discovered that there were very few overlaps between the mRNAs harboring actively translating uORFs and those sorted into the co-translational decay pathway in the majority of the studied angiosperms, suggesting that these two processes might be nearly mutually exclusive in those species. In total, our findings provide the identification of CTRD and actively translating uORFs across a broad collection of plants and provide novel insights into the important sequence features associated with these collections of mRNAs and regulatory elements, respectively.
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Affiliation(s)
- Rong Guo
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Xiang Yu
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Present address:
School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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47
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Loughran G, Li X, O’Loughlin S, Atkins JF, Baranov P. Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts. Nucleic Acids Res 2022; 51:304-314. [PMID: 36533511 PMCID: PMC9841425 DOI: 10.1093/nar/gkac1180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/08/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
A stop codon entering the ribosome A-site is normally decoded by release factors that induce release of the polypeptide. Certain factors influence the efficiency of the termination which is in competition with elongation in either the same (readthrough) or an alternative (frameshifting) reading frame. To gain insight into the competition between these processes, we monitored translation in parallel from all three reading frames downstream of stop codons while changing the nucleotide context of termination sites or altering cellular conditions (polyamine levels). We found that P-site codon identity can have a major impact on the termination efficiency of the OPRL1 stop signal, whereas for the OAZ1 ORF1 stop signal, the P-site codon mainly influences the reading frame of non-terminating ribosomes. Changes to polyamine levels predominantly influence the termination efficiency of the OAZ1 ORF1 stop signal. In contrast, increasing polyamine levels stimulate readthrough of the OPRL1 stop signal by enhancing near-cognate decoding rather than by decreasing termination efficiency. Thus, by monitoring the four competing processes occurring at stop codons we were able to determine which is the most significantly affected upon perturbation. This approach may be useful for the interrogation of other recoding phenomena where alternative decoding processes compete with standard decoding.
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Affiliation(s)
- Gary Loughran
- Correspondence may also be addressed to Gary Loughran.
| | - Xiang Li
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sinead O’Loughlin
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland,Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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48
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Abstract
Cystic fibrosis (CF) is a multiorgan disease caused by a wide variety of mutations in the cystic fibrosis transmembrane conductance regulator gene. As treatment has progressed from symptom mitigation to targeting of specific molecular defects, genetics has played an important role in identifying the proper precision therapies for each individual. Novel therapeutic approaches are focused on expanding treatment to a greater number of individuals as well as working toward a cure. This review discusses the role of genetics in our understanding of CF with a particular emphasis on how genetics informs the exciting landscape of current and novel CF therapies.
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Affiliation(s)
- Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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49
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Zhang N, Wang J, Bakker W, Zheng W, Baccaro M, Murali A, van Ravenzwaay B, Rietjens IMCM. In vitro models to detect in vivo bile acid changes induced by antibiotics. Arch Toxicol 2022; 96:3291-3303. [PMID: 36074177 PMCID: PMC9584874 DOI: 10.1007/s00204-022-03373-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022]
Abstract
Bile acid homeostasis plays an important role in many biological activities through the bile-liver-gut axis. In this study, two in vitro models were applied to further elucidate the mode of action underlying reported in vivo bile acid changes induced by antibiotics (colistin sulfate, tobramycin, meropenem trihydrate, and doripenem hydrate). 16S rRNA analysis of rat fecal samples anaerobically incubated with these antibiotics showed that especially tobramycin induced changes in the gut microbiota. Furthermore, tobramycin was shown to inhibit the microbial deconjugation of taurocholic acid (TCA) and the transport of TCA over an in vitro Caco-2 cell layer used as a model to mimic intestinal bile acid reuptake. The effects induced by the antibiotics in the in vitro model systems provide novel and complementary insight explaining the effects of the antibiotics on microbiota and fecal bile acid levels upon 28-day in vivo treatment of rats. In particular, our results provide insight in the mode(s) of action underlying the increased levels of TCA in the feces upon tobramycin exposure. Altogether, the results of the present study provide a proof-of-principle on how in vitro models can be used to elucidate in vivo effects on bile acid homeostasis, and to obtain insight in the mode(s) of action underlying the effect of an antibiotic, in this case tobramycin, on bile acid homeostasis via effects on intestinal bile acid metabolism and reuptake.
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Affiliation(s)
- Nina Zhang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Jingxuan Wang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Wouter Bakker
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Weijia Zheng
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Marta Baccaro
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | | | | | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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Palomar-Siles M, Heldin A, Zhang M, Strandgren C, Yurevych V, van Dinter JT, Engels SAG, Hofman DA, Öhlin S, Meineke B, Bykov VJN, van Heesch S, Wiman KG. Translational readthrough of nonsense mutant TP53 by mRNA incorporation of 5-Fluorouridine. Cell Death Dis 2022; 13:997. [PMID: 36433934 PMCID: PMC9700717 DOI: 10.1038/s41419-022-05431-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
Abstract
TP53 nonsense mutations in cancer produce truncated inactive p53 protein. We show that 5-FU metabolite 5-Fluorouridine (FUr) induces full-length p53 in human tumor cells carrying R213X nonsense mutant TP53. Ribosome profiling visualized translational readthrough at the R213X premature stop codon and demonstrated that FUr-induced readthrough is less permissive for canonical stop codon readthrough compared to aminoglycoside G418. FUr is incorporated into mRNA and can potentially base-pair with guanine, allowing insertion of Arg tRNA at the TP53 R213X UGA premature stop codon and translation of full-length wild-type p53. We confirmed that full-length p53 rescued by FUr triggers tumor cell death by apoptosis. FUr also restored full-length p53 in TP53 R213X mutant human tumor xenografts in vivo. Thus, we demonstrate a novel strategy for therapeutic rescue of nonsense mutant TP53 and suggest that FUr should be explored for treatment of patients with TP53 nonsense mutant tumors.
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Affiliation(s)
- Mireia Palomar-Siles
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Angelos Heldin
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Meiqiongzi Zhang
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Strandgren
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Yurevych
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jip T. van Dinter
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sem A. G. Engels
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Damon A. Hofman
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Susanne Öhlin
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Birthe Meineke
- grid.4714.60000 0004 1937 0626Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir J. N. Bykov
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Sebastiaan van Heesch
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Klas G. Wiman
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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