Global fine-tuning of translation by queuosinylation and Dnmt2-dependent tRNA methylation
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE102376 | GEO | 2019/02/13
REPOSITORIES: GEO
Similar Datasets
Project description:In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To faithfully detect Q-modification in RNAs from Schizosaccharomyces pombe and Shigella flexneri, Q-MaP-Seq was established and applied to tRNAs from S. pombe WT (AEP1) cells and Shigella flexneri WT cells and tgt∆ cells. Q-modification of in vitro-transcribed RNAs and RNAs isolated from S. pombe and S. flexneri followed by reverse transcription using the RT-active DNA polymerase variant RT-KTq I614Y and sequencing of unmodified compared to modified RNAs allowed identification of Q-sites within tRNAs.
2023-03-15 | GSE216921 | GEO
Project description:In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To investigate whether other RNAs are also Q-or preQ1-modified in Schizosaccharomyces pombe, Q-RIP-Seq was established and applied to RNAs from WT (AEP1) and qtr2∆ cells (AEP288). Metabolic labeling of RNAs with azido-propyl-preQ1 (preQ1-L1), chemical clicking of a biotin-alkyne followed by immunoprecipitation on streptavidin beads and sequencing of enriched RNAs in WT compared to qtr2∆ allowed identification of Q-modified RNAs.
2022-09-30 | GSE210404 | GEO
Project description:Queuosine (Q) is a complex tRNA modification found at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that such 7-deazaguanine-derivatives are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.
2023-09-19 | GSE236838 | GEO
Project description:Amebiasis is an intestinal disease transmitted by the protist parasite, Entamoeba histolytica, following the ingestion of contaminated food and water. Many infected patients (90%) are asymptomatic but for unknown reasons, these trophozoites can become virulent and invasive, cause amebic dysentery, and migrate to the liver, via the portal veins, where they cause hepatocellular damage. We have recently reported that Escherichia coli can modulate E.histolytica 's virulence and resistance to oxidative stress (OS) via the production of oxaloacetate. Queuosine is a naturally occurring modified nucleoside and is found in the first position of the anticodon of the transfer RNAs for Asp, Asn, His and Tyr. Lower and higher eukaryotes are supplied with queuine (the base of queuosine) in the diet or by the intestinal flora. Here, we have tested the hypothesis that queuine being a micronutrient offers an advantage to E.histolytica during OS. Queuine which is efficiently incorporated in E.histolytica’s tRNAs leads to significant modifications of the parasite’s transcriptome, to hypermethylation of C38 in tRNAAspGTC and consequently to OS resistance. While queuine leads to the translation of proteins during OS, we found that that it inhibits protein synthesis otherwise. Localization studies with an antibody against EhTGT in queuine-treated trophozoites revealed the presence of small granular structures. We have biochemically characterized the parasite’s tRNA-guanine transglycosylase (TGT), the enzyme that catalyzes the modification of Q-tRNAs. Trophozoites silenced for TGT expression have a growth defect and they are less resistant to OS compared to control trophozoites.
2021-02-18 | GSE142211 | GEO
Project description:Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. Despite decades of study, cellular roles of Q modification remain to be fully elucidated. Here we show that in human cells, Q modification specifically protects its cognate tRNAHis and tRNAAsn against cleavage by ribonucleases. We generated cell lines that contain completely depleted or fully Q-modified tRNAs. Using these resources, we found that Q modification significantly reduces angiogenin cleavage of its cognate tRNAs in vitro. Q modification does not change the cellular abundance of the cognate full-length tRNAs, but alters the cellular content of their fragments in vivo in the absence and presence of stress. Our results provide a new biological aspect of Q modification and a mechanism of how Q modification alters small RNA pool in human cells.
2018-08-10 | GSE102570 | GEO
Project description:Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas the substrate for Q-modification in tRNA in mammals is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method of biological RNA samples that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method Periodate-dependent analysis of queuosine and thio modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
2022-06-22 | GSE196016 | GEO
Project description:Cells respond to environmental stress by regulating gene expression at the level of both transcription and translation. The ~50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of tRNA wobble modifications leads to selective translation of stress response proteins from codon-biased genes. Here we show that the response of human HepG2 cells to arsenite exposure is regulated by the availability of queuine, a micronutrient and essential precursor to the wobble modification queuosine (Q) on tRNAs reading GUN codons. Among oxidizing and alkylating agents at equitoxic concentrations, arsenite exposure caused an oxidant-specific increase in Q that correlated with up-regulation of proteins from codon-biased genes involved in energy metabolism. Limiting queuine increased arsenite-induced cell death, altered translation, increased reactive oxygen species levels, and caused mitochondrial dysfunction. In addition to revealing a new epitranscriptomic facet of arsenite toxicity and response, our results highlight the mechanistic links between environmental exposures, stress tolerance, and micronutrients.
2022-06-03 | GSE205332 | GEO
Project description:Queuosine modification protects cognate tRNAs against ribonuclease cleavage
| PRJNA398048 | ENA
Project description:Cells respond to environmental stress by regulating gene expression at the level of both transcription and translation. The ~50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of tRNA wobble modifications leads to selective translation of stress response proteins from codon-biased genes. Here we show that the response of human HepG2 cells to arsenite exposure is regulated by the availability of queuine, a micronutrient and essential precursor to the wobble modification queuosine (Q) on tRNAs reading GUN codons. Among oxidizing and alkylating agents at equitoxic concentrations, arsenite exposure caused an oxidant-specific increase in Q that correlated with up-regulation of proteins from codon-biased genes involved in energy metabolism. Limiting queuine increased arsenite-induced cell death, altered translation, increased reactive oxygen species levels, and caused mitochondrial dysfunction. In addition to revealing a new epitranscriptomic facet of arsenite toxicity and response, our results highlight the mechanistic links between environmental exposures, stress tolerance, and micronutrients.
2022-08-27 | PXD030726 | Pride
Project description:Previously, combined loss of specific anticodon loop modifications was shown to impair the function of distinct tRNAs in Saccharomyces cerevisiae. Surprisingly, each scenario resulted in shared cellular phenotypes, the basis of which is unclear. To investigate how loss of different tRNA modifications can induce overlapping phenotypes, we characterized global transcription patterns of modification mutants with defects in either tRNAGlnUUG or tRNALysUUU function. We observe that the mutants share an inappropriate induction of multiple starvation responses, including derepression of glucose and nitrogen catabolite-repressed genes as well as improper activation of amino acid biosynthesis and autophagy genes, all of which occur prematurely and inadequately in exponential growth phase. We further demonstrate that improper responses to starvation as well as the propensity of the tRNA modification mutants to form protein aggregates are diminished upon overexpression of tRNAGlnUUG or tRNALysUUU, the tRNA species that lack the modifications of interest. Hence, our data suggest that global alterations in mRNA translation and proteostasis (rather than codon specific defects in translation) account for the transcriptional stress signatures that are commonly triggered by loss of anticodon modifications in different tRNAs.
2020-04-01 | GSE141887 | GEO