scholarly journals Evolutionary dynamics of abundant stop codon readthrough inAnophelesandDrosophila

2016 ◽  
Author(s):  
Irwin Jungreis ◽  
Clara S Chan ◽  
Robert M Waterhouse ◽  
Gabriel Fields ◽  
Michael F Lin ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Stop Codon ◽  
Rna Structures ◽  
Stop Codons ◽  
New Genes ◽  
Single Clade ◽  
Peroxisomal Targeting ◽  
Recent Developments ◽  
Yeast Genes ◽  
Stop Codon Readthrough

AbstractTranslational stop codon readthrough was virtually unknown in eukaryotic genomes until recent developments in comparative genomics and new experimental techniques revealed evidence of readthrough in hundreds of fly genes and several human, worm, and yeast genes. Here, we use the genomes of 21 species ofAnophelesmosquitoes and improved comparative techniques to identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector,Anopheles gambiae, and 51 additionalDrosophila melanogasterstop codons, with several cases of double and triple readthrough including readthrough of two adjacent stop codons, supporting our earlier prediction of abundant readthrough in pancrustacea genomes. Comparisons betweenAnophelesandDrosophilaallow us to transcend the static picture provided by single-clade analysis to explore the evolutionary dynamics of abundant readthrough. We find that most differences between the readthrough repertoires of the two species are due to readthrough gain or loss in existing genes, rather than to birth of new genes or to gene death; that RNA structures are sometimes gained or lost while readthrough persists; and that readthrough is more likely to be lost at TAA and TAG stop codons. We also determine which characteristic properties of readthrough predate readthrough and which are clade-specific. We estimate that there are more than 600 functional readthrough stop codons inA. gambiaeand 900 inD. melanogaster. We find evidence that readthrough is used to regulate peroxisomal targeting in two genes. Finally, we use the sequenced centipede genome to refine the phylogenetic extent of abundant readthrough.

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

Open Biology ◽  
2016 ◽  
Vol 6 (11) ◽  
pp. 160246 ◽  
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.

scholarly journals Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity

2020 ◽  
Vol 117 (36) ◽  
pp. 22167-22172
Author(s):  
Hong Zhang ◽  
Zhihui Lyu ◽  
Yongqiang Fan ◽  
Christopher R. Evans ◽  
Karl W. Barber ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Stop Codon ◽  
Single Cells ◽  
Metabolic Stress ◽  
Aminoglycoside Antibiotic ◽  
Bacterial Cells ◽  
Excess Carbon ◽  
Stop Codons ◽  
Release Factors ◽  
Stop Codon Readthrough

Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial cells. However, little is known about how environmental factors affect the level and heterogeneity of stop-codon readthrough. In this study, we have combined dual-fluorescence reporters, mass spectrometry, mathematical modeling, and single-cell approaches to demonstrate that a metabolic stress caused by excess carbon substantially increases both the level and heterogeneity of stop-codon readthrough. Excess carbon leads to accumulation of acid metabolites, which lower the pH and the activity of release factors to promote readthrough. Furthermore, our time-lapse microscopy experiments show that single cells with high readthrough levels are more adapted to severe acid stress conditions and are more sensitive to an aminoglycoside antibiotic. Our work thus reveals a metabolic stress that promotes translational heterogeneity and phenotypic diversity.

scholarly journals Evolutionary Dynamics of Abundant Stop Codon Readthrough

2016 ◽  
Vol 33 (12) ◽  
pp. 3108-3132 ◽  
Author(s):  
Irwin Jungreis ◽  
Clara S. Chan ◽  
Robert M. Waterhouse ◽  
Gabriel Fields ◽  
Michael F. Lin ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Stop Codon ◽  
Stop Codon Readthrough

scholarly journals New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae

2014 ◽  
Vol 42 (15) ◽  
pp. 10061-10072 ◽  
Author(s):  
Sandra Blanchet ◽  
David Cornu ◽  
Manuela Argentini ◽  
Olivier Namy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Stop Codon ◽  
Reporter System ◽  
Yeast Saccharomyces Cerevisiae ◽  
Systematic Analysis ◽  
Stop Codons ◽  
Nucleotide Context ◽  
Stop Codon Readthrough

AbstractStop codon readthrough may be promoted by the nucleotide environment or drugs. In such cases, ribosomes incorporate a natural suppressor tRNA at the stop codon, leading to the continuation of translation in the same reading frame until the next stop codon and resulting in the expression of a protein with a new potential function. However, the identity of the natural suppressor tRNAs involved in stop codon readthrough remains unclear, precluding identification of the amino acids incorporated at the stop position. We established an in vivo reporter system for identifying the amino acids incorporated at the stop codon, by mass spectrometry in the yeast Saccharomyces cerevisiae. We found that glutamine, tyrosine and lysine were inserted at UAA and UAG codons, whereas tryptophan, cysteine and arginine were inserted at UGA codon. The 5′ nucleotide context of the stop codon had no impact on the identity or proportion of amino acids incorporated by readthrough. We also found that two different glutamine tRNAGln were used to insert glutamine at UAA and UAG codons. This work constitutes the first systematic analysis of the amino acids incorporated at stop codons, providing important new insights into the decoding rules used by the ribosome to read the genetic code.

scholarly journals Ribosome recycling factor ABCE1 depletion inhibits nonsense-mediated mRNA decay by promoting stop codon readthrough

2019 ◽  
Author(s):  
Giuditta Annibaldis ◽  
René Dreos ◽  
Michal Domanski ◽  
Sarah Carl ◽  
Oliver Mühlemann
Keyword(s):  
Mrna Decay ◽  
Stop Codon ◽  
Translation Termination ◽  
Ribosome Profiling ◽  
List Type ◽  
Ribosome Recycling Factor ◽  
Stop Codons ◽  
Nonsense Mediated Mrna Decay ◽  
Ribosome Disassembly ◽  
Stop Codon Readthrough

SUMMARYNonsense-mediated mRNA decay (NMD) is an essential post-transcriptional surveillance pathway in vertebrates that appears to be mechanistically linked with translation termination. To gain more insight into this connection, we interfered with translation termination by depleting human cells of the ribosome recycling factor ABCE1, which resulted in an upregulation of many but not all endogenous NMD-sensitive mRNAs. Notably, the suppression of NMD on these mRNAs occurs at a step prior to their SMG6-mediated endonucleolytic cleavage. Ribosome profiling revealed that ABCE1 depletion results in ribosome stalling at stop codons and increased ribosome occupancy in 3’ UTRs, indicative of enhanced stop codon readthrough or re-initiation. Using reporter genes, we further demonstrate that the absence of ABCE1 indeed increases the rate of readthrough, which would explain the observed NMD inhibition, since enhanced readthrough has been previously shown to render NMD-sensitive transcripts resistant to NMD by displacing NMD triggering factors like UPF1 and exon junction complexes (EJCs) from the 3’ UTR. Collectively, our results show that improper ribosome disassembly interferes with proper NMD activation.HighlightsABCE1 knockdown suppresses NMD of many NMD-sensitive mRNAsThe observed NMD inhibition occurs at a stage prior to SMG6-mediated cleavage of the mRNAABCE1 depletion enhances ribosome occupancy at stop codons and in the 3’ UTRABCE1 depletion enhances readthrough of the stop codonEnhanced readthrough inhibits NMD, presumably by clearing the 3’ UTR of NMD factors

scholarly journals Eukaryotic ribosome recognizes 3 context and stimulates stop codon readthrough

2021 ◽  
Author(s):  
Elizaveta Sokolova ◽  
Tatiana Egorova ◽  
Alexey Shuvalov ◽  
Elena Alkalaeva
Keyword(s):  
18S Rrna ◽  
Stop Codon ◽  
Translation Termination ◽  
Translation System ◽  
Stop Codons ◽  
Nucleotide Context ◽  
The One ◽  
A Site ◽  
Stop Codon Readthrough ◽  
Cognate Trna

It is known that the nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3 contexts have been described that are unfavourable for translation termination; however, the exact molecular mechanism that mediates their effect 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. Our results revealed that ribosomes can independently recognize certain contexts and ignore stop codons that are followed by these sequences. Moreover, the efficiency of translation termination at the weak 3 contexts was almost equal to the one at the standard context. We propose that weak 3 contexts interact with the 18S rRNA provoking a conformational change in the U-turn-like structure of the stop codon in the A site of ribosome. This change makes incorporation of the near-cognate tRNA more preferable than recognition of the stop codon by the release factors and increases readthrough.

scholarly journals Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner

2019 ◽  
Author(s):  
Yanan Chen ◽  
Tianhui Sun ◽  
Zhuo Bi ◽  
Jian-Quan Ni ◽  
Jose C. Pastor-Pareja ◽  
...  
Keyword(s):  
Life Cycle ◽  
Premature Termination ◽  
Stop Codon ◽  
Premature Termination Codon ◽  
Anatomical Site ◽  
Stop Codons ◽  
Premature Termination Codons ◽  
Nonsense Mediated Mrna Decay ◽  
Rescue Mechanism ◽  
Stop Codon Readthrough

AbstractDespite their essential function in terminating translation, readthrough of stop codons occurs more frequently than previously supposed. However, little is known about the regulation of stop codon readthrough by anatomical site and over the life cycle of animals. Here, we developed a set of reporters to measure readthrough in Drosophila melanogaster. A focused RNAi screen in whole animals identified upf1 as a mediator of readthrough, suggesting that the stop codons in the reporters were recognized as premature termination codons (PTCs). We found readthrough rates of PTCs varied significantly throughout the life cycle of flies, being highest in older adult flies. Furthermore, readthrough rates varied dramatically by tissue and, intriguingly, were highest in fly brains, specifically neurons and not glia. This was not due to differences in reporter abundance or nonsense-mediated mRNA decay (NMD) surveillance between these tissues. Overall, our data reveal temporal and spatial variation of PTC-mediated readthrough in animals, and suggest that readthrough may be a potential rescue mechanism for PTC-harboring transcripts when the NMD surveillance pathway is inhibited.

Ectopic Transcript Analysis Indicates that Allelic Exclusion is an Important Cause of Type I Protein C Deficiency in Patients with Nonsense and Frameshift Mutations in the PROC Gene

1996 ◽  
Vol 75 (06) ◽  
pp. 870-876 ◽  
Author(s):  
José Manuel Soria ◽  
Lutz-Peter Berg ◽  
Jordi Fontcuberta ◽  
Vijay V Kakkar ◽  
Xavier Estivill ◽  
...  
Keyword(s):  
Splice Site ◽  
Protein C ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Allelic Exclusion ◽  
Polymorphism Analysis ◽  
Type I ◽  
Protein C Deficiency ◽  
Nonsense Mutations ◽  
Stop Codons

SummaryNonsense mutations, deletions and splice site mutations are a common cause of type I protein C deficiency. Either directly or indirectly by altering the reading frame, these' lesions generate or may generate premature stop codons and could therefore be expected to result in premature termination of translation. In this study, the possibility that such mutations could instead exert their pathological effects at an earlier stage in the expression pathway, through “allelic exclusion” at the RNA level, was investigated. Protein C (PROC) mRNA was analysed in seven Spanish type I protein C deficient patients heterozygous for two nonsense mutations, a 7bp deletion, a 2bp insertion and three splice site mutations. Ectopic RNA transcripts from patient and control lymphocytes were analysed by RT-PCR and direct sequencing of amplified PROC cDNA fragments. The nonsense mutations and the deletion were absent from the cDNAs indicating that only mRNA derived from the normal allele had been expressed. Similarly for the splice site mutations, only normal PROC cDNAs were obtained. In one case, exclusion of the mutated allele could be confirmed by polymorphism analysis. In contrast to these six mutations, the 2 bp insertion was not associated with loss of mRNA from the mutated allele. In this case, cDNA analysis revealed the absence of 19 bases from the PROC mRNA consistent with the generation and utilization of a cryptic splice site 3’ to the site of mutation, which would result in a frameshift and a premature stop codon. It is concluded that allelic exclusion is a common causative mechanism in those cases of type I protein C deficiency which result from mutations that introduce premature stop codons

Sign in / Sign up

Export Citation Format

Share Document