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231 results for “codon”
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages
<p><strong>Abstract</strong></p> <p>Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero- organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of Bacteria and Eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.</p> <p><strong>Repository Contents</strong></p> <p>00.description of MAGs.xlsx</p> <p>01.MAGs.zip<br> A collection of Asgardarchaeota genomes recovered in this study, i.e. The original contigs for each of the 71 MAGs (.fa files).</p> <p>02.MAG_genes.zip<br> A collection of Asgardarchaeota genome annotations (translated CDS / proteins) recovered in this study, i.e. The prokka output for each MAG (faa files)</p> <p>03.trees.zip<br> A collection of Newick tree files included in figures and supplementary figures in this study.</p> <p>04.Prokka_annotations.tar.gz (Added in 5 Aug, 2021)</p> <p>Prokka annotation files for the 71 Asgard genomes.</p>
Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
<p>Genomes and supplementary materials for Borges et al. 2021 (<strong>Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes) </strong></p>
Azithromycin Treatment for Readthrough of APC Gene Stop Codon Mutations in Familial Adenomatous Polyposis
ClinicalTrials.gov study NCT04454151. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Erythromycin Treatment for Readthrough of APC Gene Stop Codon Mutations in Familial Adenomatous Polyposis
ClinicalTrials.gov study NCT02175914. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prognostic Value of Each Codon-specific KRAS Mutation in Colorectal Cancer
ClinicalTrials.gov study NCT05657210. IPD Sharing: NO. Countries: 1. Publications: 0.
Codon and amino acid content regulate mRNA stability in mammalian cells
GEO Series GSE138292. Homo sapiens; Cricetulus griseus. 14 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Modeling ribosome dwell times and relationship with tRNA loading and codon usage in mammals (tRNA Profiling)
GEO Series GSE126382. Mus musculus. 24 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [5P-seq]
GEO Series GSE245670. Saccharomyces cerevisiae. 12 samples. Type: Other.
Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons [ncRNA-Seq]
GEO Series GSE301916. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Transcriptome analysis of polymorphic p53 codon 72 under genotoxic stress
GEO Series GSE183668. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Data from: Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates
Open the record for dataset details and reuse information.
A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [Ribo-seq]
GEO Series GSE276078. Acanthamoeba castellanii. 8 samples. Type: Other.
Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (RNA-Seq)
GEO Series GSE229671. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Combinatorial analyis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons
GEO Series GSE174329. Homo sapiens. 82 samples. Type: Expression profiling by high throughput sequencing; Other.
Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer
GEO Series GSE276695. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]
GEO Series GSE123608. Homo sapiens. 8 samples. Type: Other.
Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [mono_di_profiling]
GEO Series GSE245671. Saccharomyces cerevisiae. 18 samples. Type: Other.
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
GEO Series GSE162780. Saccharomyces cerevisiae W303. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons [RNA-Seq]
GEO Series GSE301914. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Bi-directional ribosome scanning controls the stringency of start codon selection
GEO Series GSE176058. Mus musculus; Homo sapiens. 22 samples. Type: Other.
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International Brain Laboratory public data
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OpenNeuro
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