Author response: Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides

AbstractStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418 treatment globally alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1).

Download Full-text

Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides

eLife ◽

10.7554/elife.52611 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 19

Author(s):

Jamie R Wangen ◽

Rachel Green

Keyword(s):

Mammalian Cells ◽

Stop Codon ◽

Translation Termination ◽

Premature Termination Codon ◽

Ribosome Profiling ◽

Termination Codon ◽

Stop Codons ◽

Genome Wide ◽

A Genome

Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418-induced miscoding alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1).

Download Full-text

Stop Codon Context-Specific Induction of Translational Readthrough

Biomolecules ◽

10.3390/biom11071006 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1006

Author(s):

Mirco Schilff ◽

Yelena Sargsyan ◽

Julia Hofhuis ◽

Sven Thoms

Keyword(s):

Premature Termination ◽

Stop Codon ◽

Premature Termination Codon ◽

Termination Codon ◽

Reporter System ◽

Pathogenic Variants ◽

Drug Concentrations ◽

Translational Readthrough ◽

Monogenic Diseases ◽

Codon Context

Premature termination codon (PTC) mutations account for approximately 10% of pathogenic variants in monogenic diseases. Stimulation of translational readthrough, also known as stop codon suppression, using translational readthrough-inducing drugs (TRIDs) may serve as a possible therapeutic strategy for the treatment of genetic PTC diseases. One important parameter governing readthrough is the stop codon context (SCC) – the stop codon itself and the nucleotides in the vicinity of the stop codon on the mRNA. However, the quantitative influence of the SCC on treatment outcome and on appropriate drug concentrations are largely unknown. Here, we analyze the readthrough-stimulatory effect of various readthrough-inducing drugs on the SCCs of five common premature termination codon mutations of PEX5 in a sensitive dual reporter system. Mutations in PEX5, encoding the peroxisomal targeting signal 1 receptor, can cause peroxisomal biogenesis disorders of the Zellweger spectrum. We show that the stop context has a strong influence on the levels of readthrough stimulation and impacts the choice of the most effective drug and its concentration. These results highlight potential advantages and the personalized medicine nature of an SCC-based strategy in the therapy of rare diseases.

Download Full-text

The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code

Open Biology ◽

10.1098/rsob.160246 ◽

2016 ◽

Vol 6 (11) ◽

pp. 160246 ◽

Cited By ~ 15

Author(s):

Julia Hofhuis ◽

Fabian Schueren ◽

Christopher Nötzel ◽

Thomas Lingner ◽

Jutta Gärtner ◽

...

Keyword(s):

Malate Dehydrogenase ◽

Stop Codon ◽

Protein Isoforms ◽

Translational Readthrough ◽

Peroxisomal Targeting ◽

Codon Context ◽

Targeting Signal ◽

Stop Codon Readthrough ◽

Insight Into ◽

Actual Ratio

Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (e x tended protein) to ‘normal' MDH1 is dependent on the cell type. In human cells, arginine and tryptophan are co-encoded by the MDH1x UGA stop codon. Readthrough is controlled by the 7-nucleotide high-readthrough stop codon context without contribution of the subsequent 50 nucleotides encoding the extension. All vertebrate MDH1x is directed to peroxisomes via a hidden peroxisomal targeting signal (PTS) in the readthrough extension, which is more highly conserved than the extension of lactate dehydrogenase B. The hidden PTS of non-mammalian MDH1x evolved to be more efficient than the PTS of mammalian MDH1x. These results provide insight into the genetic and functional co-evolution of these dually localized dehydrogenases.

Download Full-text

Author response: Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

10.7554/elife.60498.sa2 ◽

2020 ◽

Author(s):

Hajnalka L Pálinkás ◽

Angéla Békési ◽

Gergely Róna ◽

Lőrinc Pongor ◽

Gábor Papp ◽

...

Keyword(s):

Distribution Patterns ◽

Author Response ◽

Human Dna ◽

Genome Wide

Download Full-text

MORFEE: a new tool for detecting and annotating single nucleotide variants creating premature ATG codons from VCF files

10.1101/2020.03.29.012054 ◽

2020 ◽

Cited By ~ 1

Author(s):

Dylan Aïssi ◽

Omar Soukarieh ◽

Carole Proust ◽

Beatrice Jaspard-Vinassa ◽

Pierre Fautrad ◽

...

Keyword(s):

Stop Codon ◽

Association Studies ◽

Premature Stop Codon ◽

Open Reading Frames ◽

Strong Impact ◽

Genome Wide Association Studies ◽

Single Nucleotide Variants ◽

Functional Variants ◽

Genome Wide ◽

Upstream Open Reading Frames

AbstractSummaryVariants in 5’UTR regions that create upstream translation initiation AUG codons are a class of neglected non coding variations. When they associate with a premature stop codon and create upstream open reading frames (uORFs) whose translation competes with that of natural proteins, they can have strong impact on human diseases. We here describe MORFEE, a new bioinformatics tool that detects, annotates and predicts, from a standard VCF file, the creation of uORF by any 5’UTR variants on uORF creation. MORFEE was applied to two genomic resources and identified candidate functional variants that could explain statistical association signals observed in the context of Genome Wide Association Studies or could be responsible for rare forms of diseases. In conclusion MORFEE is an easy-to-use tool complementary to existing ones that can help resolving genetic investigations that remained so far unfruitful.Availability and implementationMORFEE is written in R with code and package available at https://github.com/daissi/[email protected]; [email protected]

Download Full-text

Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria

eLife ◽

10.7554/elife.62655 ◽

2020 ◽

Vol 9 ◽

Author(s):

Kyle Mangano ◽

Tanja Florin ◽

Xinhao Shao ◽

Dorota Klepacki ◽

Irina Chelysheva ◽

...

Keyword(s):

Antimicrobial Peptide ◽

Stop Codon ◽

Translation Termination ◽

Bacterial Cells ◽

Release Factor ◽

Translation Arrest ◽

Genome Wide Analysis ◽

Genome Wide ◽

Exit Tunnel ◽

Unique Mechanism

Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.

Download Full-text