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Dataset results
41 results for “tRNA synthetase”
In silico subcellular targeting predictions for cytosolic aminoacyl tRNA-synthetases (aaRS) in parasitic plants
<p>Eukaryotic nuclear genomes often encode distinct sets of protein translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This phenomenon raises questions about why multiple translation systems are maintained even though they are capable of comparable functions, and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in land plants because translation machinery, including aminoacyl-tRNA synthetases (aaRS), is often dual-targeted to both the plastids and mitochondria. These two organelles have quite different metabolisms, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in other eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic translation machinery across a broad sampling of angiosperms, including non-photosynthetic (heterotrophic) plant species with reduced rates of plastid gene expression to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of bacterial-like enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism.</p>
Finding orthologs for aminoacyl tRNA synthetases in parasitic plants
<p>Eukaryotic nuclear genomes often encode distinct sets of protein translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This phenomenon raises questions about why multiple translation systems are maintained even though they are capable of comparable functions, and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in land plants because translation machinery, including aminoacyl-tRNA synthetases (aaRS), is often dual-targeted to both the plastids and mitochondria. These two organelles have quite different metabolisms, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in other eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic translation machinery across a broad sampling of angiosperms, including non-photosynthetic (heterotrophic) plant species with reduced rates of plastid gene expression to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of bacterial-like enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism.</p>
Evolutionary rate analysis of aminoacyl tRNA synthetases
<p>Eukaryotic nuclear genomes often encode distinct sets of protein translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This phenomenon raises questions about why multiple translation systems are maintained even though they are capable of comparable functions, and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in land plants because translation machinery, including aminoacyl-tRNA synthetases (aaRS), is often dual-targeted to both the plastids and mitochondria. These two organelles have quite different metabolisms, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in other eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic translation machinery across a broad sampling of angiosperms, including non-photosynthetic (heterotrophic) plant species with reduced rates of plastid gene expression to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of bacterial-like enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism.</p>
Finding orthologs for aminoacyl tRNA synthetases in parasitic plants
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In silico subcellular targeting predictions for cytosolic aminoacyl tRNA-synthetases (aaRS) in parasitic plants
Open the record for dataset details and reuse information.
Evolutionary rate analysis of aminoacyl tRNA synthetases
Open the record for dataset details and reuse information.
The Structural Basis of the Genetic Code: Amino Acid Recognition by Aminoacyl-tRNA Synthetases
<p>Data sets for the characterization of amino acid recognition in aminoacyl-tRNA synthetases:</p> <ul> <li>multiple-sequence alignment files in FASTA format</li> <li>Excel tables to infer original sequence positions from renumbered positions</li> </ul> <p>Accompanying the paper: <a href="https://www.biorxiv.org/content/10.1101/606459v1">https://www.biorxiv.org/content/10.1101/606459v1</a></p>
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
<p>Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in <em>Sileneae </em>species and <em>Arabidopsis thaliana. W</em>e investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage <em>Sileneae</em> that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement.</p> <p>Nikon .nd2 raw microscopy files for the transient expression and imaging of predicted transit peptides and colocalization assays in <em>N. benthamiana</em> epithelial cells. The amino acid sequence plus 10 upstream amino acids of the protein body were fused to GFP and co-transfected with an eqFP611-tagged transit peptide from a known mitochondrially localized protein (isovaleryl-CoA dehydrogenase).</p>
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
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RNA immunoprecipitation and sequencing of aminoacyl-tRNA synthetase-specific genes
GEO Series GSE120182. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response
GEO Series GSE315548. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Targeted degradation of extracellular mitochondrial aspartyl-tRNA synthetase modulates immune responses in bacterial pneumonia
GEO Series GSE260733. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Angiogenesis induced by aminoacyl-tRNA synthetase deficiency is dependent on AAR but not UPR pathways
GEO Series GSE130193. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
NCP26 is a potent prolyl-tRNA synthetase inhibitor and induces pro- apoptotic responses with in vivo potency in multiple myeloma. Single-cell RNA-seq data BM samples.
GEO Series GSE186447. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing.
NCP26 is a potent prolyl-tRNA synthetase inhibitor and induces pro- apoptotic responses with in vivo potency in multiple myeloma. Bulk RNA-seq data.
GEO Series GSE186445. Homo sapiens. 66 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional dysregulation by a nucleus-localized aminoacyl-tRNA synthetase is associated with Charcot-Marie-Tooth neuropathy
GEO Series GSE125311. Drosophila melanogaster. 17 samples. Type: Expression profiling by high throughput sequencing.
T cell-Macrophage Interactions Mediate Innate and Adaptive Immune Responses in Histidyl-tRNA Synthetase-Induced Myositis
GEO Series GSE229059. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing; Other.
Seryl-tRNA synthetase inhibits Wnt signaling and breast cancer progression and metastasis
GEO Series GSE264557. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
NCP26 is a potent prolyl-tRNA synthetase inhibitor and induces pro- apoptotic responses with in vivo potency in multiple myeloma
GEO Series GSE186448. Homo sapiens. 92 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.