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154 results for “ribosome biogenesis”
YBEY as a ribosome biogenesis factor
<p>The ultraconserved RNA-binding protein YbeY has been associated with ribosomal RNA processing in numerous bacteria. However, mechanistic understanding of its function is still lacking, in particular in the light of the generally poor conservation of rRNA processing pathways across the bacterial kingdom. By leveraging the fact that YbeY homologues are wide-spread not only in bacteria but also in most eukaryotes harbouring bacteria-derived organelles, we addressed the functional significance of this protein in the highly divergent genetic system of human mitochondria.</p> <p>Mammalian mitochondrial rRNAs are known to be fully processed by dedicated RNase P and RNase Z enzymes, making additional ribonucleases superfluous. Indeed, <em>YBEY</em> knockout mitochondria were found to process all their ribosomal RNAs normally. Nevertheless, in the absence of YBEY, the mitochondrial small subunit (SSU) rRNA showed significant destabilisation, associated with a late SSU assembly defect. Component analysis identified a significant depletion of the mitoribosomal protein uS11m and several other, structurally dependent SSU constituents forming the platform and the head of the subunit. Our biochemical and genetic data suggest that this assembly defect renders the mitochondrial SSU initiation-incompetent, leading to a nearly complete translational shutdown in the mitochondrial compartment. Consequently, <em>YBEY</em> KO cells completely lose the ability to carry out oxidative phosphorylation.</p> <p>Coimmunoprecipitation and FLIM-FRET <em>in situ</em> interactomics, further supported by analyses in a heterologous system, identified direct and tight interactions between YBEY, uS11m and p32, a deeply conserved RNA-binding protein involved in mitoribosome assembly in a variety of eukaryotes. The three proteins form together stable and stoichiometric complexes. We propose that YBEY, together with p32, helps to efficiently deliver and/or correctly position uS11m on the nascent mitochondrial SSU in order to complete the assembly of the platform. Based on existing data, this YBEY function appears to be broadly conserved.</p>
An in vivo stable isotope labeling method to investigate individual matrix protein synthesis, ribosomal biogenesis, and chondrocyte proliferation in murine articular cartilage
<p>These experiments have used a stable-isotope method using <em>in vivo</em> deuterium oxide labeling and mass spectrometry to measure protein concentration, protein half-life, cell proliferation, and ribosomal biogenesis in a single sample of murine articular cartilage. We hypothesized that a 60-day labeling period would capture age-related declines in cartilage matrix protein content, protein synthesis rates, and chondrocyte proliferation. Knee cartilage was isolated from 25- and 90-week-old female C57BL/6J mice treated with deuterium oxide for 15, 30, 45 and 60 days. We measured protein abundance and half-lives using high resolution accurate mass spectrometry (HRAM) and d2ome data processing software. </p>
Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins
<p>The ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), which form the ancient ribosomal stalk, were discovered decades ago but their functions remain mysterious. We had previously shown that RPLP1/2 are exquisitely required for replication of dengue virus (DENV) and other mosquito-borne flaviviruses. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We evaluated viral and cellular translation in RPLP1/2-depleted cells using ribosome profiling and found that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). We also find that RPLP1/2 depletion impacts a ribosome density for a small subset of cellular mRNAs. Importantly, the polarity of ribosomes on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, implying a role for RPLP1/2 in multipass transmembrane protein biogenesis. These analyses of viral and host RNAs converge to implicate RPLP1/2 as functionally important for ribosomes to elongate through ORFs encoding multiple TMDs. We suggest that the effect of RPLP1/2 at TMD associated pauses is mediated by improving the efficiency of co-translational folding and subsequent protein stability.</p>
Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins
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A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence (CRISPRi screen)
GEO Series GSE232856. Homo sapiens. 4 samples. Type: Other.
Post-transcriptional regulation of Ribosome Biogenesis during differentiation [dRNA-seq]
GEO Series GSE214874. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]
GEO Series GSE107327. Escherichia coli. 14 samples. Type: Expression profiling by high throughput sequencing.
An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [786-O]
GEO Series GSE270847. Homo sapiens. 4 samples. Type: Other.
Dot6 is a major regulator of cell size and a transcriptional activator of ribosome biogenesis in the opportunistic yeast Candida albicans
GEO Series GSE119089. Candida albicans. 3 samples. Type: Expression profiling by array.
Cancer-associated fibroblast-secreted FGF2 faliciates gastric cancer cell proliferation by enhancing ribosome biogenesis
GEO Series GSE249966. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Current androgen deprivation induces androgen receptor-independent prostate cancer via HGF and Wnt activation to foster nuclear export and ribosome biogenesis [scRNA-Seq]
GEO Series GSE226555. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells
GEO Series GSE67609. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Crac analysis of the Bud22 ribosome biogenesis factor
GEO Series GSE214203. Saccharomyces cerevisiae. 2 samples. Type: Other.
Simultaneous activation of Tor and suppression of ribosome biogenesis by TRIM-NHL proteins promotes terminal differentiation
GEO Series GSE218205. Drosophila melanogaster. 6 samples. Type: Expression profiling by high throughput sequencing.
Combined targeting poly (ADP-ribose) polymerase and receptor tyrosine kinase inhibits ovarian clear cell carcinoma progression through disrupted ribosome biogenesis
GEO Series GSE264286. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells
GEO Series GSE218290. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide reporter screen for transcriptional regulators of ribosome biogenesis genes and ribosomal protein genes
GEO Series GSE207900. synthetic construct. 19 samples. Type: Other.
The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis
GEO Series GSE291748. Escherichia coli. 4 samples. Type: Other.
Ribosomal biogenesis genes play an essential and p53-independent role in pancreas development
GEO Series GSE39399. Danio rerio. 16 samples. Type: Expression profiling by array.
A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [aramis mRNA IP]
GEO Series GSE190969. Drosophila melanogaster. 9 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.