An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA415988 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6225330_1.fastq.gz | Fastqsanger.gz | |||
| SRR6225330_2.fastq.gz | Fastqsanger.gz | |||
| SRR6225340_1.fastq.gz | Fastqsanger.gz | |||
| SRR6225340_2.fastq.gz | Fastqsanger.gz | |||
| SRR6225350_1.fastq.gz | Fastqsanger.gz |
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Project description:mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes. Here we show that Pelo is required for mammalian epidermal homeostasis. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.
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Project description:mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes. Here we show that Pelo is required for mammalian epidermal homeostasis. Conditional deletion in murine epidermal stem cells expressing Lrig1 results in hyperproliferation and abnormal differentiation, whereas deletion in other stem cells does not. Loss of Pelo results in truncated ribosome footprints and global upregulation of translation. Translational inhibition by rapamycin-mediated down regulation of mTOR rescues the epidermal phenotype. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.
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Project description:Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. In a genetic screen in E. coli, we discovered a novel rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNA) to rescue upstream ribosomes. SmrB is recruited by ribosome collisions. Cryo-EM structures of collided disomes from E. coli and B. subtilis reveal interactions between the 30S subunits and a possible SmrB binding site. These findings show that ribosome collisions trigger ribosome rescue in bacteria and reveal the mechanism by which this occurs.
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Project description:To identify evolutionarily conserved Beta-catenin protein interactions, Beta-catenin mRNA from various metazoans was injected into Xenopus embryos and immunopurified at gastrula stage. Beta-catenin complexes were then separated on an SDS-PAGE gel and subjected mass spectrometric analysis
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Project description:The choroid plexus produces cerebrospinal fluid (CSF) by transport of electrolytes and water from the vasculature to the brain ventricles. The choroid plexus plays additional roles in brain development and homeostasis by secreting neurotrophic molecules, and by serving as a CSF-blood barrier and immune interface. Prior studies have identified transporters on the epithelial cells that transport water and ions into the ventricles and tight junctions involved in the CSF-blood barrier. Yet, how the choroid plexus epithelial cells maintain the brain ventricle system and control brain physiology remain unresolved. To provide novel insights into the physiological roles of the choroid plexus, we use juvenile and adult zebrafish as model systems. Upon histological and transcriptomic analyses, we first identified that the zebrafish choroid plexus is highly conserved with the mammalian choroid plexus and that it expresses all transporters necessary for CSF secretion. Using novel genetic lines, we also identified that the choroid plexus secretes proteins into the CSF. Next, we generated a transgenic line allowing us to ablate specifically the epithelial cells in the choroid plexus. Using the ablation system, we identified a reduction of the ventricular sizes, but no alterations of the CSF-blood barrier. Altogether, our findings identified that the zebrafish choroid plexus is evolutionarily conserved and critical for maintaining the size and homeostasis of the brain ventricles.
2024-05-06 | GSE246851 | GEO
Project description:The genetic bases for most human sleep disorders and for variation in human sleep quantity and quality are largely unknown. Using the zebrafish, a diurnal vertebrate, to investigate the genetic regulation of sleep, we found that epidermal growth factor receptor (EGFR) signaling is necessary and sufficient for normal sleep levels and is required for the normal homeostatic response to sleep deprivation. We observed that EGFR signaling promotes sleep via mitogen-activated protein kinase/extracellular signal-regulated kinase and RFamide neuropeptide signaling and that it regulates RFamide neuropeptide expression and neuronal activity. Consistent with these findings, analysis of a large cohort of human genetic data from participants of European ancestry revealed that common variants in genes within the EGFR signaling pathway are associated with variation in human sleep quantity and quality. These results indicate that EGFR signaling and its downstream pathways play a central and ancient role in regulating sleep and provide new therapeutic targets for sleep disorders.
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Project description:MotivationProtein synthesis is a non-equilibrium process, meaning that the speed of translation can influence the ability of proteins to fold and function. Assuming that structurally similar proteins fold by similar pathways, the profile of translation speed along an mRNA should be evolutionarily conserved between related proteins to direct correct folding and downstream function. The only evidence to date for such conservation of translation speed between homologous proteins has used codon rarity as a proxy for translation speed. There are, however, many other factors including mRNA structure and the chemistry of the amino acids in the A- and P-sites of the ribosome that influence the speed of amino acid addition.ResultsRibosome profiling experiments provide a signal directly proportional to the underlying translation times at the level of individual codons. We compared ribosome occupancy profiles (extracted from five different large-scale yeast ribosome profiling studies) between related protein domains to more directly test if their translation schedule was conserved. Our analysis reveals that the ribosome occupancy profiles of paralogous domains tend to be significantly more similar to one another than to profiles of non-paralogous domains. This trend does not depend on domain length, structural classes, amino acid composition, or sequence similarity. Our results indicate that entire ribosome occupancy profiles and not just rare codon locations are conserved between even distantly related domains in yeast, providing support for the hypothesis that translation schedule is conserved between structurally related domains to retain folding pathways and facilitate efficient folding.AvailabilityPython3 code is available on GitHub at https://github.com/DanNissley/Compare-ribosome-occupancy-profiles.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8317121 | biostudies-literature
Project description:Ribosome biogenesis, a complex multistep process, results in correct folding of rRNAs, incorporation of >50 ribosomal proteins, and their maturation. Deficiencies in ribosome biogenesis may result in varied faults in translation of mRNAs causing cellular toxicities and ribosomopathies in higher organisms. How cells ensure quality control in ribosome biogenesis for the fidelity of its complex function remains unclear. Using Escherichia coli, we show that initiator tRNA (i-tRNA), specifically the evolutionarily conserved three consecutive GC base pairs in its anticodon stem, play a crucial role in ribosome maturation. Deficiencies in cellular contents of i-tRNA confer cold sensitivity and result in accumulation of ribosomes with immature 3' and 5' ends of the 16S rRNA. Overexpression of i-tRNA in various strains rescues biogenesis defects. Participation of i-tRNA in the first round of initiation complex formation licenses the final steps of ribosome maturation by signaling RNases to trim the terminal extensions of immature 16S rRNA.
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