1
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Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S. The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. Nat Chem Biol 2024; 20:877-884. [PMID: 38172604 DOI: 10.1038/s41589-023-01521-0] [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: 04/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1.
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Affiliation(s)
- João P L Coelho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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2
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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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3
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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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4
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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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5
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Fansler MM, Mitschka S, Mayr C. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 2024; 15:4050. [PMID: 38744866 PMCID: PMC11094166 DOI: 10.1038/s41467-024-48254-9] [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: 08/30/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
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Affiliation(s)
- Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine Mayr
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA.
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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6
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Lukhovitskaya N, Brown K, Hua L, Pate AE, Carr JP, Firth AE. A novel ilarvirus protein CP-RT is expressed via stop codon readthrough and suppresses RDR6-dependent RNA silencing. PLoS Pathog 2024; 20:e1012034. [PMID: 38814986 PMCID: PMC11166343 DOI: 10.1371/journal.ppat.1012034] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
Ilarviruses are a relatively understudied but important group of plant RNA viruses that includes a number of crop pathogens. Their genomes comprise three RNA segments encoding two replicase subunits, movement protein, coat protein (CP), and (in some ilarvirus subgroups) a protein that suppresses RNA silencing. Here we report that, in many ilarviruses, RNA3 encodes an additional protein (termed CP-RT) as a result of ribosomal readthrough of the CP stop codon into a short downstream readthrough (RT) ORF. Using asparagus virus 2 as a model, we find that CP-RT is expressed in planta where it functions as a weak suppressor of RNA silencing. CP-RT expression is essential for persistent systemic infection in leaves and shoot apical meristem. CP-RT function is dependent on a putative zinc-finger motif within RT. Replacing the asparagus virus 2 RT with the RT of an ilarvirus from a different subgroup restored the ability to establish persistent infection. These findings open up a new avenue for research on ilarvirus silencing suppression, persistent meristem invasion and vertical transmission.
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Affiliation(s)
- Nina Lukhovitskaya
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Lei Hua
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Adrienne E. Pate
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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7
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Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Jagannathan S. Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575080. [PMID: 38260612 PMCID: PMC10802582 DOI: 10.1101/2024.01.10.575080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nonsense variants underlie many genetic diseases. The phenotypic impact of nonsense variants is determined by Nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). NMD activity varies across transcripts and cellular contexts via poorly understood mechanisms. Here, by leveraging human genetic datasets, we uncover that the amino acid preceding the PTC dramatically affects NMD activity in human cells. We find that glycine codons in particular support high levels of NMD and are enriched before PTCs but depleted before normal termination codons (NTCs). Gly-PTC enrichment is most pronounced in human genes that tolerate loss-of-function variants. This suggests a strong biological impact for Gly-PTC in ensuring robust elimination of potentially toxic truncated proteins from non-essential genes. Biochemical assays revealed that the peptide release rate during translation termination is highly dependent on the identity of the amino acid preceding the stop codon. This release rate is the most critical feature determining NMD activity across our massively parallel reporter assays. Together, we conclude that NMD activity is significantly modulated by the "window of opportunity" offered by translation termination kinetics. Integrating the window of opportunity model with the existing framework of NMD would enable more accurate nonsense variant interpretation in the clinic.
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Affiliation(s)
- Divya Kolakada
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mlana Lore
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amy E. Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A. Cortázar
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Marcin P. Sajek
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Lead contact
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8
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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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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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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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11
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May GE, Akirtava C, Agar-Johnson M, Micic J, Woolford J, McManus J. Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning. eLife 2023; 12:e69611. [PMID: 37227054 PMCID: PMC10259493 DOI: 10.7554/elife.69611] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/24/2023] [Indexed: 05/26/2023] Open
Abstract
Upstream open-reading frames (uORFs) are potent cis-acting regulators of mRNA translation and nonsense-mediated decay (NMD). While both AUG- and non-AUG initiated uORFs are ubiquitous in ribosome profiling studies, few uORFs have been experimentally tested. Consequently, the relative influences of sequence, structural, and positional features on uORF activity have not been determined. We quantified thousands of yeast uORFs using massively parallel reporter assays in wildtype and ∆upf1 yeast. While nearly all AUG uORFs were robust repressors, most non-AUG uORFs had relatively weak impacts on expression. Machine learning regression modeling revealed that both uORF sequences and locations within transcript leaders predict their effect on gene expression. Indeed, alternative transcription start sites highly influenced uORF activity. These results define the scope of natural uORF activity, identify features associated with translational repression and NMD, and suggest that the locations of uORFs in transcript leaders are nearly as predictive as uORF sequences.
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Affiliation(s)
- Gemma E May
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Matthew Agar-Johnson
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - John Woolford
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Joel McManus
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
- Computational Biology Department, Carnegie Mellon UniversityPittsburghUnited States
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12
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Rodnina MV. Decoding and Recoding of mRNA Sequences by the Ribosome. Annu Rev Biophys 2023; 52:161-182. [PMID: 37159300 DOI: 10.1146/annurev-biophys-101922-072452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Faithful translation of messenger RNA (mRNA) into protein is essential to maintain protein homeostasis in the cell. Spontaneous translation errors are very rare due to stringent selection of cognate aminoacyl transfer RNAs (tRNAs) and the tight control of the mRNA reading frame by the ribosome. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, reprogram the ribosome to make intentional mistakes and produce alternative proteins from the same mRNA. The hallmark of recoding is the change of ribosome dynamics. The signals for recoding are built into the mRNA, but their reading depends on the genetic makeup of the cell, resulting in cell-specific changes in expression programs. In this review, I discuss the mechanisms of canonical decoding and tRNA-mRNA translocation; describe alternative pathways leading to recoding; and identify the links among mRNA signals, ribosome dynamics, and recoding.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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13
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Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 (BETHESDA, MD.) 2023; 13:jkad028. [PMID: 36748990 PMCID: PMC10085805 DOI: 10.1093/g3journal/jkad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.
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Affiliation(s)
- Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Han Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alison Pidoux
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn 74081, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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14
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Abstract
Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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15
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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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16
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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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17
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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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18
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Heldin A, Cancer M, Palomar-Siles M, Öhlin S, Zhang M, Sun-Zhang A, Mariani A, Liu J, Bykov VJN, Wiman KG. Novel compounds that synergize with aminoglycoside G418 or eRF3 degraders for translational readthrough of nonsense mutant TP53 and PTEN. RNA Biol 2023; 20:368-383. [PMID: 37339263 DOI: 10.1080/15476286.2023.2222250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/22/2023] Open
Abstract
The TP53 and PTEN tumour suppressor genes are inactivated by nonsense mutations in a significant fraction of human tumours. TP53 nonsense mutatant tumours account for approximately one million new cancer cases per year worldwide. We have screened chemical libraries with the aim of identifying compounds that induce translational readthrough and expression of full-length p53 protein in cells with nonsense mutation in this gene. Here we describe two novel compounds with readthrough activity, either alone or in combination with other known readthrough-promoting substances. Both compounds induced levels of full-length p53 in cells carrying R213X nonsense mutant TP53. Compound C47 showed synergy with the aminoglycoside antibiotic and known readthrough inducer G418, whereas compound C61 synergized with eukaryotic release factor 3 (eRF3) degraders CC-885 and CC-90009. C47 alone showed potent induction of full-length PTEN protein in cells with different PTEN nonsense mutations. These results may facilitate further development of novel targeted cancer therapy by pharmacological induction of translational readthrough.
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Affiliation(s)
- Angelos Heldin
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Matko Cancer
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Mireia Palomar-Siles
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Öhlin
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Meiqiongzi Zhang
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Sun-Zhang
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Anna Mariani
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Jianping Liu
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Vladimir J N Bykov
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Klas G Wiman
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
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19
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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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20
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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21
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Ho AT, Hurst LD. Stop codon usage as a window into genome evolution: mutation, selection, biased gene conversion and the TAG paradox. Genome Biol Evol 2022; 14:6648529. [PMID: 35867377 PMCID: PMC9348620 DOI: 10.1093/gbe/evac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an unusual window into the forces operating on what are ostensibly functionally identical residues. Across genomes and between isochores within the human genome, TGA usage increases with G + C content but, with a common G + C → A + T mutation bias, this cannot be explained by mutation bias-drift equilibrium. Increased usage of TGA in G + C-rich genomes or genomic regions is also unlikely to reflect selection for the optimal stop codon, as TAA appears to be universally optimal, probably because it has the lowest read-through rate. Despite TAA being favored by selection and mutation bias, as with codon usage bias G + C pressure is the prime determinant of between-species TGA usage trends. In species with strong G + C-biased gene conversion (gBGC), such as mammals and birds, the high usage and conservation of TGA is best explained by an A + T → G + C repair bias. How to explain TGA enrichment in other G + C-rich genomes is less clear. Enigmatically, across bacterial and archaeal species and between human isochores TAG usage is mostly unresponsive to G + C pressure. This unresponsiveness we dub the TAG paradox as currently no mutational, selective, or gBGC model provides a well-supported explanation. That TAG does increase with G + C usage across eukaryotes makes the usage elsewhere yet more enigmatic. We suggest resolution of the TAG paradox may provide insights into either an unknown but common selective preference (probably at the DNA/RNA level) or an unrecognized complexity to the action of gBGC.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, UK
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22
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Biziaev N, Sokolova E, Yanvarev DV, Toropygin IY, Shuvalov A, Egorova T, Alkalaeva E. Recognition of 3' nucleotide context and stop codon readthrough are determined during mRNA translation elongation. J Biol Chem 2022; 298:102133. [PMID: 35700825 PMCID: PMC9272376 DOI: 10.1016/j.jbc.2022.102133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
The nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts that are unfavorable for translation termination have been described; however, the exact molecular mechanism that mediates their effects remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. We developed an approach to estimate the level of stop codon readthrough in the absence of eukaryotic release factors (eRFs). In this system, the stop codon is recognized by the suppressor or near-cognate tRNAs. We observed that in the absence of eRFs, readthrough occurs in a 3′ nucleotide context-dependent manner, and the main factors determining readthrough efficiency were the type of stop codon and the sequence of the 3′ nucleotides. Moreover, the efficiency of translation termination in weak 3′ contexts was almost equal to that in the tested standard context. Therefore, the ability of eRFs to recognize stop codons and induce peptide release is not affected by mRNA context. We propose that ribosomes or other participants of the elongation cycle can independently recognize certain contexts and increase the readthrough of stop codons. Thus, the efficiency of translation termination is regulated by the 3′ nucleotide context following the stop codon and depends on the concentrations of eRFs and suppressor/near-cognate tRNAs.
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Affiliation(s)
- Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Dmitry V Yanvarev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ilya Yu Toropygin
- Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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23
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Ho AT, Hurst LD. Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection. PLoS Biol 2022; 20:e3001588. [PMID: 35550630 PMCID: PMC9129041 DOI: 10.1371/journal.pbio.3001588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
The assumption that conservation of sequence implies the action of purifying selection is central to diverse methodologies to infer functional importance. GC-biased gene conversion (gBGC), a meiotic mismatch repair bias strongly favouring GC over AT, can in principle mimic the action of selection, this being thought to be especially important in mammals. As mutation is GC→AT biased, to demonstrate that gBGC does indeed cause false signals requires evidence that an AT-rich residue is selectively optimal compared to its more GC-rich allele, while showing also that the GC-rich alternative is conserved. We propose that mammalian stop codon evolution provides a robust test case. Although in most taxa TAA is the optimal stop codon, TGA is both abundant and conserved in mammalian genomes. We show that this mammalian exceptionalism is well explained by gBGC mimicking purifying selection and that TAA is the selectively optimal codon. Supportive of gBGC, we observe (i) TGA usage trends are consistent at the focal stop codon and elsewhere (in UTR sequences); (ii) that higher TGA usage and higher TAA→TGA substitution rates are predicted by a high recombination rate; and (iii) across species the difference in TAA <-> TGA substitution rates between GC-rich and GC-poor genes is largest in genomes that possess higher between-gene GC variation. TAA optimality is supported both by enrichment in highly expressed genes and trends associated with effective population size. High TGA usage and high TAA→TGA rates in mammals are thus consistent with gBGC’s predicted ability to “drive” deleterious mutations and supports the hypothesis that sequence conservation need not be indicative of purifying selection. A general trend for GC-rich trinucleotides to reside at frequencies far above their mutational equilibrium in high recombining domains supports the generality of these results.
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Affiliation(s)
- Alexander Thomas Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- * E-mail:
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24
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Krebs SK, Rakotoarinoro N, Stech M, Zemella A, Kubick S. A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality. Front Bioeng Biotechnol 2022; 10:873906. [PMID: 35573244 PMCID: PMC9098822 DOI: 10.3389/fbioe.2022.873906] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein’s coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyrCUA were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
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Affiliation(s)
- Simon K. Krebs
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin, Berlin, Germany
| | - Nathanaël Rakotoarinoro
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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25
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Kute PM, Soukarieh O, Tjeldnes H, Trégouët DA, Valen E. Small Open Reading Frames, How to Find Them and Determine Their Function. Front Genet 2022; 12:796060. [PMID: 35154250 PMCID: PMC8831751 DOI: 10.3389/fgene.2021.796060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
Advances in genomics and molecular biology have revealed an abundance of small open reading frames (sORFs) across all types of transcripts. While these sORFs are often assumed to be non-functional, many have been implicated in physiological functions and a significant number of sORFs have been described in human diseases. Thus, sORFs may represent a hidden repository of functional elements that could serve as therapeutic targets. Unlike protein-coding genes, it is not necessarily the encoded peptide of an sORF that enacts its function, sometimes simply the act of translating an sORF might have a regulatory role. Indeed, the most studied sORFs are located in the 5′UTRs of coding transcripts and can have a regulatory impact on the translation of the downstream protein-coding sequence. However, sORFs have also been abundantly identified in non-coding RNAs including lncRNAs, circular RNAs and ribosomal RNAs suggesting that sORFs may be diverse in function. Of the many different experimental methods used to discover sORFs, the most commonly used are ribosome profiling and mass spectrometry. These can confirm interactions between transcripts and ribosomes and the production of a peptide, respectively. Extensions to ribosome profiling, which also capture scanning ribosomes, have further made it possible to see how sORFs impact the translation initiation of mRNAs. While high-throughput techniques have made the identification of sORFs less difficult, defining their function, if any, is typically more challenging. Together, the abundance and potential function of many of these sORFs argues for the necessity of including sORFs in gene annotations and systematically characterizing these to understand their potential functional roles. In this review, we will focus on the high-throughput methods used in the detection and characterization of sORFs and discuss techniques for validation and functional characterization.
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Affiliation(s)
- Preeti Madhav Kute
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Omar Soukarieh
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Håkon Tjeldnes
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - David-Alexandre Trégouët
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- *Correspondence: Eivind Valen,
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26
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Ho AT, Hurst LD. Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage. Mol Biol Evol 2022; 39:msab326. [PMID: 34751397 PMCID: PMC8789281 DOI: 10.1093/molbev/msab326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3'untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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27
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Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
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Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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28
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Galibert L, Hyvönen A, Eriksson RAE, Mattola S, Aho V, Salminen S, Albers JD, Peltola SK, Weman S, Nieminen T, Ylä-Herttuala S, Lesch HP, Vihinen-Ranta M, Airenne KJ. Functional roles of the membrane-associated AAV protein MAAP. Sci Rep 2021; 11:21698. [PMID: 34737404 PMCID: PMC8568889 DOI: 10.1038/s41598-021-01220-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
With a limited coding capacity of 4.7 kb, adeno-associated virus (AAV) genome has evolved over-lapping genes to maximise the usage of its genome. An example is the recently found ORF in the cap gene, encoding membrane-associated accessory protein (MAAP), located in the same genomic region as the VP1/2 unique domain, but in a different reading frame. This 13 KDa protein, unique to the dependovirus genus, is not homologous to any known protein. Our studies confirm that MAAP translation initiates from the first CTG codon found in the VP1 ORF2. We have further observed MAAP localised in the plasma membrane, in the membranous structures in close proximity to the nucleus and to the nuclear envelope by co-transfecting with plasmids encoding the wild-type AAV (wt-AAV) genome and adenovirus (Ad) helper genes. While keeping VP1/2 protein sequence identical, both inactivation and truncation of MAAP translation affected the emergence and intracellular distribution of the AAV capsid proteins. We have demonstrated that MAAP facilitates AAV replication and has a role in controlling Ad infection. Additionally, we were able to improve virus production and capsid integrity through a C-terminal truncation of MAAP while other modifications led to increased packaging of contaminating, non-viral DNA. Our results show that MAAP plays a significant role in AAV infection, with profound implications for the production of therapeutic AAV vectors.
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Affiliation(s)
| | - Amira Hyvönen
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland ,grid.511728.8FinVector, Kuopio, Finland
| | - Reetta A. E. Eriksson
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland ,grid.9668.10000 0001 0726 2490A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Salla Mattola
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Vesa Aho
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Sami Salminen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland
| | | | | | - Saija Weman
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Tiina Nieminen
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland ,grid.9668.10000 0001 0726 2490A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XGene Therapy Unit and Research Center, Kuopio University Hospital, Kuopio, Finland
| | - Hanna P. Lesch
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Maija Vihinen-Ranta
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland
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29
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Zinshteyn B, Sinha NK, Enam SU, Koleske B, Green R. Translational repression of NMD targets by GIGYF2 and EIF4E2. PLoS Genet 2021; 17:e1009813. [PMID: 34665823 PMCID: PMC8555832 DOI: 10.1371/journal.pgen.1009813] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/29/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Translation of messenger RNAs (mRNAs) with premature termination codons produces truncated proteins with potentially deleterious effects. This is prevented by nonsense-mediated mRNA decay (NMD) of these mRNAs. NMD is triggered by ribosomes terminating upstream of a splice site marked by an exon-junction complex (EJC), but also acts on many mRNAs lacking a splice junction after their termination codon. We developed a genome-wide CRISPR flow cytometry screen to identify regulators of mRNAs with premature termination codons in K562 cells. This screen recovered essentially all core NMD factors and suggested a role for EJC factors in degradation of PTCs without downstream splicing. Among the strongest hits were the translational repressors GIGYF2 and EIF4E2. GIGYF2 and EIF4E2 mediate translational repression but not mRNA decay of a subset of NMD targets and interact with NMD factors genetically and physically. Our results suggest a model wherein recognition of a stop codon as premature can lead to its translational repression through GIGYF2 and EIF4E2.
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Affiliation(s)
- Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Niladri K. Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Syed Usman Enam
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Benjamin Koleske
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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30
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Functional Restoration of CFTR Nonsense Mutations in Intestinal Organoids. J Cyst Fibros 2021; 21:246-253. [PMID: 34666947 DOI: 10.1016/j.jcf.2021.09.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pharmacotherapies for people with cystic fibrosis (pwCF) who have premature termination codons (PTCs) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are under development. Thus far, clinical studies focused on compounds that induce translational readthrough (RT) at the mRNA PTC location. Recent studies using primary airway cells showed that PTC functional restoration can be achieved through combining compounds with multiple mode-of-actions. Here, we assessed induction of CFTR function in PTC-containing intestinal organoids using compounds targeting RT, nonsense mRNA mediated decay (NMD) and CFTR protein modulation. METHODS Rescue of PTC CFTR protein was assessed by forskolin-induced swelling of 12 intestinal organoid cultures carrying distinct PTC mutations. Effects of compounds on mRNA CFTR level was assessed by RT-qPCRs. RESULTS Whilst response varied between donors, significant rescue of CFTR function was achieved for most donors with the quintuple combination of a commercially available pharmacological equivalent of the RT compound (ELX-02-disulfate or ELX-02ds), NMD inhibitor SMG1i, correctors VX-445 and VX-661 and potentiator VX-770. The quintuple combination of pharmacotherapies reached swelling quantities higher than the mean swelling of three VX-809/VX-770-rescued F508del/F508del organoid cultures, indicating level of rescue is of clinical relevance as VX-770/VX-809-mediated F508del/F508del rescue in organoids correlate with substantial improvement of clinical outcome. CONCLUSIONS Whilst variation in efficacy was observed between genotypes as well as within genotypes, the data suggests that strong pharmacological rescue of PTC requires a combination of drugs that target RT, NMD and protein function.
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31
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Zhao Y, Lindberg BG, Esfahani SS, Tang X, Piazza S, Engström Y. Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development. BMC Biol 2021; 19:185. [PMID: 34479564 PMCID: PMC8417969 DOI: 10.1186/s12915-021-01106-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background A number of cellular processes have evolved in metazoans that increase the proteome repertoire in relation to the genome, such as alternative splicing and translation recoding. Another such process, translational stop codon readthrough (SCR), generates C-terminally extended protein isoforms in many eukaryotes, including yeast, plants, insects, and humans. While comparative genome analyses have predicted the existence of programmed SCR in many species including humans, experimental proof of its functional consequences are scarce. Results We show that SCR of the Drosophila POU/Oct transcription factor Ventral veins lacking/Drifter (Vvl/Dfr) mRNA is prevalent in certain tissues in vivo, reaching a rate of 50% in the larval prothoracic gland. Phylogenetically, the C-terminal extension is conserved and harbors intrinsically disordered regions and amino acid stretches implied in transcriptional activation. Elimination of Vvl/Dfr translational readthrough by CRISPR/Cas9 mutagenesis changed the expression of a large number of downstream genes involved in processes such as chromatin regulation, neurogenesis, development, and immune response. As a proof-of-principle, we demonstrate that the C-terminal extension of Vvl/Dfr is necessary for correct timing of pupariation, by increasing the capacity to regulate its target genes. The extended Vvl/Dfr isoform acts in synergy with the transcription factor Molting defective (Mld) to increase the expression and biosynthesis of the steroid hormone ecdysone, thereby advancing pupariation. Consequently, late-stage larval development was prolonged and metamorphosis delayed in vvl/dfr readthrough mutants. Conclusions We demonstrate that translational recoding of a POU/Oct transcription factor takes place in a highly tissue-specific and temporally controlled manner. This dynamic and regulated recoding is necessary for normal expression of a large number of genes involved in many cellular and developmental processes. Loss of Vvl/Dfr translational readthrough negatively affects steroid hormone biosynthesis and delays larval development and progression into metamorphosis. Thus, this study demonstrates how SCR of a transcription factor can act as a developmental switch in a spatiotemporal manner, feeding into the timing of developmental transitions between different life-cycle stages. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01106-0.
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Affiliation(s)
- Yunpo Zhao
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Department of Molecular Biology, Umeå University, SE-901 87, Umeå, SE, Sweden
| | - Bo Gustav Lindberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Shiva Seyedoleslami Esfahani
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Xiongzhuo Tang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Stefano Piazza
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Research and Innovation Centre, Fondazione Edmund Mach, via E Mach 1, 38010, San Michele a/Adige, Italy
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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32
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Kantaputra PN, Dejkhamron P, Intachai W, Ngamphiw C, Kawasaki K, Ohazama A, Krisanaprakornkit S, Olsen B, Tongsima S, Ketudat Cairns JR. Juberg-Hayward syndrome is a cohesinopathy, caused by mutation in ESCO2. Eur J Orthod 2021; 43:45-50. [PMID: 32255174 DOI: 10.1093/ejo/cjaa023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Juberg-Hayward syndrome (JHS; MIM 216100) is a rare autosomal recessive malformation syndrome, characterized by cleft lip/palate, microcephaly, ptosis, short stature, hypoplasia or aplasia of thumbs, and dislocation of radial head and fusion of humerus and radius leading to elbow restriction. OBJECTIVE To report for the first time the molecular aetiology of JHS. PATIENT AND METHODS Clinical and radiographic examination, whole exome sequencing, Sanger sequencing, mutant protein model construction, and in situ hybridization of Esco2 expression in mouse embryos were performed. RESULTS Clinical findings of the patient consisted of repaired cleft lip/palate, microcephaly, ptosis, short stature, delayed bone age, hypoplastic fingers and thumbs, clinodactyly of the fifth fingers, and humeroradial synostosis leading to elbow restriction. Intelligence is normal. Whole exome sequencing of the whole family showed a novel homozygous base substitution c.1654C>T in ESCO2 of the proband. The sister was homozygous for the wildtype variant. Parents were heterozygous for the mutation. The mutation is predicted to cause premature stop codon p.Arg552Ter. Mutations in ESCO2, a gene involved in cohesin complex formation, are known to cause Roberts/SC phocomelia syndrome. Roberts/SC phocomelia syndrome and JHS share similar clinical findings, including autosomal recessive inheritance, short stature, cleft lip/palate, severe upper limb anomalies, and hypoplastic digits. Esco2 expression during the early development of lip, palate, eyelid, digits, upper limb, and lower limb and truncated protein model are consistent with the defect. CONCLUSIONS Our study showed that Roberts/SC phocomelia syndrome and JHS are allelic and distinct entities. This is the first report demonstrating that mutation in ESCO2 causes JHS, a cohesinopathy.
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Affiliation(s)
- Piranit Nik Kantaputra
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand.,Dentaland Clinic, Chiang Mai, Thailand
| | - Prapai Dejkhamron
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Worrachet Intachai
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Katsushige Kawasaki
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Atsushi Ohazama
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Suttichai Krisanaprakornkit
- Center of Excellence in Oral Biology, Chiang Mai University, Chiang Mai, Thailand.,Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | - Bjorn Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Sissades Tongsima
- National Biobank of Thailand, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jame R Ketudat Cairns
- School of Chemistry, Institute of Science, and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Bartoschek MD, Ugur E, Nguyen TA, Rodschinka G, Wierer M, Lang K, Bultmann S. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res 2021; 49:e62. [PMID: 33684219 PMCID: PMC8216290 DOI: 10.1093/nar/gkab132] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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Affiliation(s)
- Michael D Bartoschek
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Enes Ugur
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tuan-Anh Nguyen
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Geraldine Rodschinka
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kathrin Lang
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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34
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Ho AT, Hurst LD. Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors. Mol Biol Evol 2021; 38:244-262. [PMID: 32797190 PMCID: PMC7783166 DOI: 10.1093/molbev/msaa210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 3' additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Corresponding author: E-mail:
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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35
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Tissue-specific dynamic codon redefinition in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2012793118. [PMID: 33500350 DOI: 10.1073/pnas.2012793118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Translational stop codon readthrough occurs in organisms ranging from viruses to mammals and is especially prevalent in decoding Drosophila and viral mRNAs. Recoding of UGA, UAG, or UAA to specify an amino acid allows a proportion of the protein encoded by a single gene to be C-terminally extended. The extended product from Drosophila kelch mRNA is 160 kDa, whereas unextended Kelch protein, a subunit of a Cullin3-RING ubiquitin ligase, is 76 kDa. Previously we reported tissue-specific regulation of readthrough of the first kelch stop codon. Here, we characterize major efficiency differences in a variety of cell types. Immunoblotting revealed low levels of readthrough in malpighian tubules, ovary, and testis but abundant readthrough product in lysates of larval and adult central nervous system (CNS) tissue. Reporters of readthrough demonstrated greater than 30% readthrough in adult brains, and imaging in larval and adult brains showed that readthrough occurred in neurons but not glia. The extent of readthrough stimulatory sequences flanking the readthrough stop codon was assessed in transgenic Drosophila and in human tissue culture cells where inefficient readthrough occurs. A 99-nucleotide sequence with potential to form an mRNA stem-loop 3' of the readthrough stop codon stimulated readthrough efficiency. However, even with just six nucleotides of kelch mRNA sequence 3' of the stop codon, readthrough efficiency only dropped to 6% in adult neurons. Finally, we show that high-efficiency readthrough in the Drosophila CNS is common; for many neuronal proteins, C-terminal extended forms of individual proteins are likely relatively abundant.
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Giess A, Torres Cleuren YN, Tjeldnes H, Krause M, Bizuayehu TT, Hiensch S, Okon A, Wagner CR, Valen E. Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. Cell Rep 2021; 31:107534. [PMID: 32320657 DOI: 10.1016/j.celrep.2020.107534] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly understood. Here, we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling us to characterize the transcriptome-wide dynamics of ribosome recruitment to mRNAs, scanning across 5' UTRs and stop codon recognition, in a higher eukaryote. We provide mechanistic evidence for ribosomes attaching to the mRNA by threading the mRNA through the small subunit. Moreover, we identify features that regulate the recruitment and processivity of scanning ribosomes and redefine optimal initiation contexts. Our approach enables deconvoluting translation initiation into separate stages and identifying regulators at each step.
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Affiliation(s)
- Adam Giess
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Yamila N Torres Cleuren
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway.
| | - Håkon Tjeldnes
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Maximilian Krause
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway; Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway
| | | | - Senna Hiensch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway
| | - Aniekan Okon
- Department Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carston R Wagner
- Department Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway; Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway.
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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Mangkalaphiban K, He F, Ganesan R, Wu C, Baker R, Jacobson A. Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. PLoS Genet 2021; 17:e1009538. [PMID: 33878104 PMCID: PMC8087045 DOI: 10.1371/journal.pgen.1009538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/30/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3'-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5' of the stop codon, six nucleotides 3' of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3'-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3'-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 had milder effects. Additionally, we found low readthrough genes to have shorter 3'-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features affecting the efficiency of translation termination and readthrough.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Richard Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Disrupting upstream translation in mRNAs is associated with human disease. Nat Commun 2021; 12:1515. [PMID: 33750777 PMCID: PMC7943595 DOI: 10.1038/s41467-021-21812-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/12/2021] [Indexed: 12/04/2022] Open
Abstract
Ribosome-profiling has uncovered pervasive translation in non-canonical open reading frames, however the biological significance of this phenomenon remains unclear. Using genetic variation from 71,702 human genomes, we assess patterns of selection in translated upstream open reading frames (uORFs) in 5’UTRs. We show that uORF variants introducing new stop codons, or strengthening existing stop codons, are under strong negative selection comparable to protein-coding missense variants. Using these variants, we map and validate gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals, respectively, and elucidate their impact on protein expression in human cells. Our results suggest translation disrupting mechanisms relating uORF variation to reduced protein expression, and demonstrate that translation at uORFs is genetically constrained in 50% of human genes. The significance of translated upstream open reading frames is not well known. Here, the authors investigate genetic variants in these regions, finding that they are under high evolutionary constraint and may contribute to disease.
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Roy G, Reier J, Garcia A, Martin T, Rice M, Wang J, Prophet M, Christie R, Dall'Acqua W, Ahuja S, Bowen MA, Marelli M. Development of a high yielding expression platform for the introduction of non-natural amino acids in protein sequences. MAbs 2021; 12:1684749. [PMID: 31775561 PMCID: PMC6927762 DOI: 10.1080/19420862.2019.1684749] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ability to genetically encode non-natural amino acids (nnAAs) into proteins offers an expanded tool set for protein engineering. nnAAs containing unique functional moieties have enabled the study of post-translational modifications, protein interactions, and protein folding. In addition, nnAAs have been developed that enable a variety of biorthogonal conjugation chemistries that allow precise and efficient protein conjugations. These are being studied to create the next generation of antibody-drug conjugates with improved efficacy, potency, and stability for the treatment of cancer. However, the efficiency of nnAA incorporation, and the productive yields of cell-based expression systems, have limited the utility and widespread use of this technology. We developed a process to isolate stable cell lines expressing a pyrrolysyl-tRNA synthetase/tRNApyl pair capable of efficient nnAA incorporation. Two different platform cell lines generated by these methods were used to produce IgG-expressing cell lines with normalized antibody titers of 3 g/L using continuous perfusion. We show that the antibodies produced by these platform cells contain the nnAA functionality that enables facile conjugations. Characterization of these highly active and robust platform hosts identified key parameters that affect nnAA incorporation efficiency. These highly efficient host platforms may help overcome the expression challenges that have impeded the developability of this technology for manufacturing proteins with nnAAs and represents an important step in expanding its utility.
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Affiliation(s)
- Gargi Roy
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jason Reier
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Andrew Garcia
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tom Martin
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Megan Rice
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jihong Wang
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Meagan Prophet
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ronald Christie
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - William Dall'Acqua
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Sanjeev Ahuja
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
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41
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Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches. Int J Mol Sci 2020; 21:ijms21249449. [PMID: 33322589 PMCID: PMC7764779 DOI: 10.3390/ijms21249449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/27/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
The fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense and stop codons. However, premature termination codons (PTCs) arising from mutations may, at low frequency, be misrecognized and result in PTC suppression, named ribosome readthrough, with production of full-length proteins through the insertion of a subset of amino acids. Since some drugs have been identified as readthrough inducers, this fidelity drawback has been explored as a therapeutic approach in several models of human diseases caused by nonsense mutations. Here, we focus on the mechanisms driving translation in normal and aberrant conditions, the potential fates of mRNA in the presence of a PTC, as well as on the results obtained in the research of efficient readthrough-inducing compounds. In particular, we describe the molecular determinants shaping the outcome of readthrough, namely the nucleotide and protein context, with the latter being pivotal to produce functional full-length proteins. Through the interpretation of experimental and mechanistic findings, mainly obtained in lysosomal and coagulation disorders, we also propose a scenario of potential readthrough-favorable features to achieve relevant rescue profiles, representing the main issue for the potential translatability of readthrough as a therapeutic strategy.
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Susorov D, Egri S, Korostelev AA. Termi-Luc: a versatile assay to monitor full-protein release from ribosomes. RNA (NEW YORK, N.Y.) 2020; 26:2044-2050. [PMID: 32817446 PMCID: PMC7668252 DOI: 10.1261/rna.076588.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 05/05/2023]
Abstract
Termination of protein biosynthesis is an essential step of gene expression, during which a complete functional protein is released from the ribosome. Premature or inefficient termination results in truncated, nonfunctional, or toxic proteins that may cause disease. Indeed, more than 10% of human genetic diseases are caused by nonsense mutations leading to premature termination. Efficient and sensitive approaches are required to study eukaryotic termination mechanisms and to identify potential therapeutics that modulate termination. Canonical radioactivity-based termination assays are complex, report on a short peptide release, and are incompatible with high-throughput screening. Here we describe a robust and simple in vitro assay to study the kinetics of full-protein release. The assay monitors luminescence upon release of nanoluciferase from a mammalian pretermination complex. The assay can be used to record time-progress curves of protein release in a high-throughput format, making it optimal for studying release kinetics and for high-throughput screening for small molecules that modulate the efficiency of termination.
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Affiliation(s)
- Denis Susorov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Shawn Egri
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Annibaldis G, Domanski M, Dreos R, Contu L, Carl S, Kläy N, Mühlemann O. Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay. Nucleic Acids Res 2020; 48:10259-10279. [PMID: 32941650 PMCID: PMC7544199 DOI: 10.1093/nar/gkaa758] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cleavage. ABCE1 depletion caused ribosome stalling at termination codons (TCs) and increased ribosome occupancy in 3′ UTRs, implying enhanced TC readthrough. ABCE1 knockdown indeed increased the rate of readthrough and continuation of translation in different reading frames, providing a possible explanation for the observed NMD inhibition, since enhanced readthrough displaces NMD activating proteins from the 3′ UTR. Our results indicate that stalling at TCs triggers ribosome collisions and activates ribosome quality control. Collectively, we show that improper translation termination can lead to readthrough of the TC, presumably due to ribosome collisions pushing the stalled ribosomes into the 3′ UTR, where it can resume translation in-frame as well as out-of-frame.
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Affiliation(s)
- Giuditta Annibaldis
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, CH-3012 Bern, Switzerland
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Lara Contu
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, CH-3012 Bern, Switzerland
| | - Sarah Carl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Nina Kläy
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Poly(A)-Binding Protein Regulates the Efficiency of Translation Termination. Cell Rep 2020; 33:108399. [PMID: 33207198 DOI: 10.1016/j.celrep.2020.108399] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 09/01/2020] [Accepted: 10/27/2020] [Indexed: 11/21/2022] Open
Abstract
Multiple factors influence translation termination efficiency, including nonsense codon identity and immediate context. To determine whether the relative position of a nonsense codon within an open reading frame (ORF) influences termination efficiency, we quantitate the production of prematurely terminated and/or readthrough polypeptides from 26 nonsense alleles of 3 genes expressed in yeast. The accumulation of premature termination products and the extent of readthrough for the respective premature termination codons (PTCs) manifest a marked dependence on PTC proximity to the mRNA 3' end. Premature termination products increase in relative abundance, whereas readthrough efficiencies decrease progressively across different ORFs, and readthrough efficiencies for a PTC increase in response to 3' UTR lengthening. These effects are eliminated and overall translation termination efficiency decreases considerably in cells harboring pab1 mutations. Our results support a critical role for poly(A)-binding protein in the regulation of translation termination and also suggest that inefficient termination is a trigger for nonsense-mediated mRNA decay (NMD).
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Sokolova EE, Vlasov PK, Egorova TV, Shuvalov AV, Alkalaeva EZ. The Influence of A/G Composition of 3' Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes. Mol Biol 2020. [DOI: 10.1134/s0026893320050088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kantaputra PN, Dejkhamron P, Tongsima S, Ngamphiw C, Intachai W, Ngiwsara L, Sawangareetrakul P, Svasti J, Olsen B, Cairns JRK, Bumroongkit K. Juberg-Hayward syndrome and Roberts syndrome are allelic, caused by mutations in ESCO2. Arch Oral Biol 2020; 119:104918. [PMID: 32977150 DOI: 10.1016/j.archoralbio.2020.104918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/10/2020] [Accepted: 09/06/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Juberg-Hayward syndrome (JHS; MIM 216100) is a rare autosomal recessive malformation syndrome, characterized by cleft lip/palate, microcephaly, ptosis, hypoplasia or aplasia of thumbs, short stature, dislocation of radial head, and fusion of humerus and radius leading to elbow restriction. A homozygous mutation in ESCO2 has recently been reported to cause Juberg-Hayward syndrome. Our objective was to investigate the molecular etiology of Juberg-Hayward syndrome in two affected Lisu tribe brothers. MATERIALS AND METHODS Two patients, the unaffected parents, and two unaffected siblings were studied. Clinical and radiographic examination, whole exome sequencing, Sanger sequencing, Western blot analysis, and chromosome testing were performed. RESULTS Two affected brothers had characteristic features of Juberg-Hayward syndrome, except for the absence of microcephaly. The elder brother had bilateral cleft lip and palate, short stature, humeroradial synostosis, and simple partial seizure with secondary generalization. The younger brother had unilateral cleft lip and palate, short stature, and dislocation of radial heads. The homozygous (c.1654C > T; p.Arg552Ter) mutation in ESCO2 was identified in both patients. The other unaffected members of the family were heterozygous for the mutation. The presence of humeroradial synostosis and radial head dislocation in the same family is consistent with both being in the same spectrum of forearm malformations. Chromosome testing of the affected patients showed premature centromere separation. Western blot analysis showed reduced amount of truncated protein. CONCLUSION Our findings confirm that a homozygous mutation in ESCO2 is the underlying cause of Juberg-Hayward syndrome. Microcephaly does not appear to be a consistent feature of the syndrome.
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Affiliation(s)
- Piranit Nik Kantaputra
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand; Dentaland Clinic, Chiang Mai, Thailand.
| | - Prapai Dejkhamron
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Worrachet Intachai
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | - Lukana Ngiwsara
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | - Bjorn Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - James R Ketudat Cairns
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand; School of Chemistry, Institute of Science, and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kanokkan Bumroongkit
- Department of Anatomy, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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Adachi H, Yu YT. Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent. RNA (NEW YORK, N.Y.) 2020; 26:1247-1256. [PMID: 32434780 PMCID: PMC7430670 DOI: 10.1261/rna.076042.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 05/26/2023]
Abstract
We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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48
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Huang X, Chen R, Sun M, Peng Y, Pu Q, Yuan Y, Chen G, Dong J, Du F, Cui X, Tang Z. Frame-shifted proteins of a given gene retain the same function. Nucleic Acids Res 2020; 48:4396-4404. [PMID: 32187359 PMCID: PMC7192591 DOI: 10.1093/nar/gkaa169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Frameshift mutations are generally considered to be lethal because it could result in radical changes of the protein sequence behind. However, the protein of frameshift mutants of a type I toxin (ibsc) was found to be still toxic to bacteria, retaining the similar function as wild-type protein to arrest the cellular growth by impairing the membrane's integrity. Additionally, we have verified that this observation is not an individual event as the same phenomenon had been found in other toxins subsequently. After analyzing the coding sequence of these genes, we proposed a hypothesis to search this kind of hidden gene, through which a dihydrofolate reductase-encoding gene (dfrB3) was found out. Like the wild-type reductase, both +1 and -1 frame-shifted proteins of dfrB3 gene were also proved to catalyze the reduction of dihydrofolate to tetrahydrofolate by using NADPH.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Rong Chen
- Ethnomedicine College, Chengdu University of Traditional Chinese Medicine, Chengdu 610041, P. R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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49
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Kramarski L, Arbely E. Translational read-through promotes aggregation and shapes stop codon identity. Nucleic Acids Res 2020; 48:3747-3760. [PMID: 32128584 PMCID: PMC7144920 DOI: 10.1093/nar/gkaa136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/07/2020] [Accepted: 02/22/2020] [Indexed: 12/14/2022] Open
Abstract
Faithful translation of genetic information depends on the ability of the translational machinery to decode stop codons as termination signals. Although termination of protein synthesis is highly efficient, errors in decoding of stop codons may lead to the synthesis of C-terminally extended proteins. It was found that in eukaryotes such elongated proteins do not accumulate in cells. However, the mechanism for sequestration of C-terminally extended proteins is still unknown. Here we show that 3′-UTR-encoded polypeptides promote aggregation of the C-terminally extended proteins, and targeting to lysosomes. We demonstrate that 3′-UTR-encoded polypeptides can promote different levels of protein aggregation, similar to random sequences. We also show that aggregation of endogenous proteins can be induced by aminoglycoside antibiotics that promote stop codon read-through, by UAG suppressor tRNA, or by knokcdown of release factor 1. Furthermore, we find correlation between the fidelity of termination signals, and the predicted propensity of downstream 3′-UTR-encoded polypeptides to form intrinsically disordered regions. Our data highlight a new quality control mechanism for elimination of C-terminally elongated proteins.
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Affiliation(s)
- Lior Kramarski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Eyal Arbely
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.,Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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50
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Seoighe C, Kiniry SJ, Peters A, Baranov PV, Yang H. Selection Shapes Synonymous Stop Codon Use in Mammals. J Mol Evol 2020; 88:549-561. [PMID: 32617614 DOI: 10.1007/s00239-020-09957-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
Abstract
Phylogenetic models of the evolution of protein-coding sequences can provide insights into the selection pressures that have shaped them. In the application of these models synonymous nucleotide substitutions, which do not alter the encoded amino acid, are often assumed to have limited functional consequences and used as a proxy for the neutral rate of evolution. The ratio of nonsynonymous to synonymous substitution rates is then used to categorize the selective regime that applies to the protein (e.g., purifying selection, neutral evolution, diversifying selection). Here, we extend the Muse and Gaut model of codon evolution to explore the extent of purifying selection acting on substitutions between synonymous stop codons. Using a large collection of coding sequence alignments, we estimate that a high proportion (approximately 57%) of mammalian genes are affected by selection acting on stop codon preference. This proportion varies substantially by codon, with UGA stop codons far more likely to be conserved. Genes with evidence of selection acting on synonymous stop codons have distinctive characteristics, compared to unconserved genes with the same stop codon, including longer [Formula: see text] untranslated regions (UTRs) and shorter mRNA half-life. The coding regions of these genes are also much more likely to be under strong purifying selection pressure. Our results suggest that the preference for UGA stop codons found in many multicellular eukaryotes is selective rather than mutational in origin.
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Affiliation(s)
- Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland.
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew Peters
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Haixuan Yang
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
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