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Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

ABSTRACT: Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

PROVIDER: PRJNA661272 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10042149.fastq.gz	Fastqsanger.gz
	SRR10042150.fastq.gz	Fastqsanger.gz
	SRR10042151.fastq.gz	Fastqsanger.gz
	SRR10042152.fastq.gz	Fastqsanger.gz
	SRR10042153.fastq.gz	Fastqsanger.gz

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Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

Project description:Proteostasis must be finely tuned in the nervous system, as it represents an essential feature of neurodevelopment, and dominant pathology in neurodegenerative disease. At the gateway of proteostasis is the ribosome; however, the architecture of ribosomal complexes in the developing mammalian brain has not been visualized. In this study, we analyze the molecular architecture of ex vivo embryonic and perinatal mouse neocortical ribosomes, revealing Ebp1 as a 60S peptide tunnel exit binding factor at near-atomic resolution by multiparticle cryo-electron microscopy. The impact of Ebp1 on the neuronal proteome was analyzed by pSILAC and BONCAT coupled mass spectrometry, implicating Ebp1 in neurite outgrowth proteostasis, with in vivo embryonic Ebp1 knockdown resulting in neurite outgrowth dysregulation. This study constitutes the first near-atomic resolution structure of actively translating ribosomes ex vivo from the nervous system, and visualizes Ebp1 as a chaperone of protein synthesis at the 60S peptide tunnel exit in neocortical neurogenesis.

2021-01-04 | PXD014841 | Pride

Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

2021-01-04 | PXD014740 | Pride

Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.

Project description:Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development.

| S-EPMC8163098 | biostudies-literature

Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-03-23 | GSE157425 | GEO

RNA-Seq analysis of total mouse neocortex during development

Project description:We report the quantification of steady-state mRNA coding for ribosomal proteins, translation-associated proteins, and Ebp1 (Pa2g4) in mouse total neocortex brain lysates at embryonic days 12.5, 14, 15.5, 17 and postnatal day 0

2021-03-23 | GSE136199 | GEO

Streptomyces cavourensis strain:60S

Project description:Streptomyces cavourensis strain:60S Genome sequencing

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P5 mouse neocortex

Project description:P5 mouse neocortex

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The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation

Project description:In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Unlike canonical assembly factors, which associate exclusively with pre-60S subunits, we observed that Reh1 sediments with polysomes in addition to free 60S subunits. We therefore investigated the intriguing possibility that Reh1 remains associated with 60S subunits after the release of the anti-association factor Tif6 and after subunit joining. Here, we show that Reh1-bound nascent 60S subunits associate with 40S subunits to form actively translating ribosomes.

2024-01-24 | GSE246163 | GEO

High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.

Project description:While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.

2017-10-04 | GSE83821 | GEO

Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation

Project description:Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. Comprehensive transcriptome analysis was employed to validate the capacity of three prioritized compounds to remodel the ER proteostasis environment, and to assess the prefential activation of ATF6 transcriptional targets relative to targets of the IRE1/XBP1s and PERK arms of the UPR. HEK293T-Rex and HEK293-DAX cells were treated for 6 hr with vehicle (DMSO), 1 ÂµM Tg, 10 mM TMP (in HEK293DAX), or 10 ÂµM 132, 147 or 263 in biological triplicate at 37 ÌC

2016-07-21 | E-GEOD-84636 | biostudies-arrayexpress

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