Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE246163 | GEO | 2024/01/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Pol5 is required for recycling of small subunit biogenesis factors and for formation of the polypeptide exit tunnel of the large ribosomal subunit

Project description:More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a strictly hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5’ external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5’ ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.

2019-11-05 | GSE132973 | GEO

The RNA helicase Dbp10 coordinates assembly factor association with PTC formation during ribosome biogenesis

Project description:During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10. Our data suggest that Dbp10’s helicase activity generates a crucial framework for assembly factor docking thereby permitting the progression of pre-60S maturation

2024-05-22 | PXD046068 | Pride

Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis

Project description:Assembly of eukaryotic ribosomes begins in the nucleolus, a compartmentalized membraneless organelle. Although the two ribosomal subunits, 40S and 60S, assemble independently, it remains unknown if these particles are physically sorted as they assemble and how they partition from the central chromatin compartment into the outer nucleolar regions, where maturation occurs. In this study, we show that nucleophosmin specifically mediates the assembly of nascent 60S subunits and that this specificity is determined by its chromatin localization at the rDNA sites encoding for 60S subunit rRNA. Nucleophosmin dissociates from chromatin to bind nascent 60S subunits, causing their partitioning away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. This directs translocation of nascent 60S subunits towards the nucleophosmin-rich granular component, where biogenesis continues. Notably, this compartmentalization increases the efficiency of 60S subunit assembly, specifically the incorporation of the 60S domain III. Our data reveal that the chromatin localization of nucleophosmin determines its specificity in sorting and coordinates the movement of ribosomal subunits into specialized assembly compartments.

2023-03-01 | GSE156203 | GEO

The RNA helicases Has1, Mak5 and Spb4 mediate diverse functions at distinct regions of pre-ribosomal complexes

Project description:Assembly of eukaryotic ribosomal subunits is a highly dynamic and energy-consuming process involving numerous structural and compositional changes. Here, we identify the pre-ribosomal binding sites of three ATP-dependent RNA helicases Has1, Mak5 and Spb4 and by elucidating the precise targets of these enzymes, we uncover direct roles of Has1 in mediating release of the U14 snoRNA and dissociation of a cluster of early pre-60S biogenesis factors. We further discover pre-rRNA remodelling by Mak5 enables recruitment of the ribosomal protein Rpl10 in the cytoplasm and show that binding of Spb4 to a molecular hinge at the base of ES27 facilitates binding of the export adaptor Arx1 to pre-60S complexes. Our data highlight RNA helicases as key regulators of critical events during ribosome biogenesis and provide novel insights into the structural remodelling events that take place during assembly of the ribosomal subunits.

2018-12-19 | GSE109216 | GEO

The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly

Project description:Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center and is responsible for stabilizing interactions between the 5’ and 3’ ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation.

2021-08-18 | GSE160734 | GEO

The RNA helicase Dbp7 promotes domain VI compaction and stabilization of inter-domain interactions during early 60S assembly

2021-08-16 | GSE161347 | GEO

Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation

Project description:Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic by two mechanisms: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.

2021-12-08 | GSE184331 | GEO

Rbp95 binds 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation

Project description:Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here we introduce Rbp95, a constituent of early pre-60S particles, as a novel ribosome assembly factor that likely already binds before the 90S to pre-60S transition. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members, and to ribosomal protein Rpl3. Notably, the RNA-binding protein Rbp95 associates with helix H95 in the 3’ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. In the absence of Rbp95, proteins binding in proximity to helix H95 are less efficiently recruited to early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the formation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex in the 90S to pre-60S transition and in promoting pre-rRNA folding events within pre-60S particles that facilitate the recruitment of subsequent assembly factors.

2022-10-13 | PXD030106 | Pride

The translation release factor methyltransferase Mtq2-Trm112 is required for ribosome biogenesis

Project description:The Mtq2-Trm112 methyltransferase is known to modify the translational eukaryotic release factor eRF1 on the glutamine side chain of a universally conserved GGQ motif, which is essential to translation termination. The exact role of eRF1 methylation remains unknown. As the deletion of MTQ2 leads to severe growth impairment in S. cerevisiae, we have investigated its role further. Here we report an unexpected function of Mtq2 in ribosome biogenesis. We reveal that Mtq2 is part of nuclear precursor ribosomes to 60S subunits, and we demonstrate that its catalytic activity is required for the stable production of mature 5.8S and 25S rRNAs and for pre-60S export. Consistently, in the absence of Mtq2 function pre-60S subunits enriched in the export factors Nmd3 and Arx1 accumulate in the nucleus. We conclude that, in addition to its role as a translation terminator modification enzyme, Mtq2 is a ribosome assembly factor which is important for late-stage large ribosomal subunit formation.

2020-10-12 | PXD018733 | Pride

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data