Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The roles of GTPases in biogenesis of the large ribosomal subunit

ABSTRACT: Ribosomes are ribonucleoprotein complexes responsible for protein synthesis, and their biogenesis is a complex, highly orchestrated process. Formation of the ribosomal subunits is coordinated by trans-acting ribosome biogenesis factors (RBFs) that mediate ribosomal RNA (rRNA) modification, folding and processing, as well as the incorporation and positioning of ribosomal proteins (RPs). GTPases are among the RBFs that consume energy to drive structural rearrangements of pre-ribosomal particles, and several of these enzymes play important roles in assembly of the large subunit. Protein-RNA crosslinking approaches were used to identify GNL3L binding sites on pre-ribosomes and map RNA contact sites on the GTPase. The findings of this study support the involvement of GNL3L in large subunit biogenesis and provide new insights into its functions in this process.

ORGANISM(S): Homo sapiens

PROVIDER: GSE302147 | GEO | 2026/03/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Distinct steps of nuclear maturation of human pre-60S complexes require the activity of GTPases, including GNL3L

Project description:Production of the eukaryotic ribosomal subunits (40S and 60S) is a highly dynamic process in which numerous assembly factors coordinate structural rearrangements of pre-ribosomal complexes to achieve their mature, functional architectures. Across the domains of life, GTPases leverage their functions as molecular switches to induce conformational changes that drive key steps in subunit maturation. Three GTPases, GTPBP4, GNL2 and GNL3 have been detected in nucleolar/nucleoplasmic human pre-60S complexes. Here we compositionally analyze the pre-ribosomal particles associated with each of these GTPases and demonstrate the requirement of these enzymes, and their abilities to bind and hydrolyze GTP, for distinct steps in pre-ribosomal RNA processing. We further reveal that the GNL3 paralogue, GNL3L, also associates with pre-ribosomes, and we map RNA contact sites on GNL3L as well as GNL3L binding sites on pre-rRNAs. Lack of GNL3L impairs synthesis of the 60S rRNAs and expression of GTPase inactive GNL3L causes defects in early steps of pre-rRNA processing. Impaired GTP hydrolysis by GNL3L leads to its accumulation on pre-60S particles, together with other assembly factors with proximal binding sites. Our data further demonstrate that the GTPase activity of GNL3L is required for maintaining 60S subunit levels, protein synthesis and cellular proliferation.

2026-03-09 | PXD068314 | Pride

The 40S-LARP1 complex reprograms the cellular translatome upon mTOR inhibition to preserve the protein synthetic capacity

Project description:Ribosomes execute the transcriptional program in every cell. Critical to sustain nearly all cellular activities, ribosome biogenesis requires the translation of ~200 factors of which 80 are ribosomal proteins (RPs). As ribosome synthesis depends on RP mRNAs translation, a priority within the translatome architecture should exist to ensure the preservation of ribosome biogenesis capacity, particularly under adverse growth conditions. Here we show that under critical metabolic constraints characterized by mTOR inhibition, LARP1 complexed with the 40S subunit protects from ribophagy the mRNAs regulon for ribosome biogenesis and protein synthesis, acutely preparing the translatome to promptly resume ribosomes production after growth conditions return permissive. Characterizing the LARP1-protected translatome revealed a set of 5’TOP transcript isoforms other than RPs involved in energy production and in mitochondrial function, among other processes, indicating that the mTOR-LARP1-5’TOP axis acts at the translational level as a primary guardian of the cellular anabolic capacity

2021-10-30 | GSE186779 | GEO

Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein in filamentous fungi

Project description:The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into rRNA are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, and up-regulated expression in response to abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 interacted with the unassembled small ribosomal subunit protein, PlRPS15, of the uS19 family. PlRPS15 contained a eukaryote-specific N-terminal extension that mediated the interaction. The phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g., growth and ribosome biogenesis defects). PlCYP5 maintained the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botytis cinerea, and Metarhizium anisopliae were identified. Notably, the interaction of their homologs corresponding to the PlCYP5-PlRPS15 pattern existed in three filamentous fungi, while lacked in other species. In summary, our data disclosed a special RP dedicated chaperone system in filamentous fungi, in which cyclophilin was enlisted to perform the chaperone funtion.

2021-07-10 | GSE179712 | GEO

Ribosome customization and functional diversification amongst P-stalk proteins regulate late poxvirus protein synthesis

Project description:Growing evidence suggests that ribosomes selectively regulate translation of specific mRNA subsets. Here, quantitative proteomics and cryo-electron microscopy demonstrated that poxvirus infection does not alter ribosomal subunit protein (RP) composition but skews 40S rotation states and displaces the 40S head domain. Genetic knockout screens employing metabolic assays and a dual-reporter virus further identified two RPs that selectively regulate non-canonical translation of late poxvirus mRNAs which contain unusual 5 polyA-leaders: RACK1 and RPLP2. RACK1 is a component of the altered 40S head domain while RPLP2 is a subunit of the P-stalk, wherein RPLP0 anchors two heterodimers of RPLP1 and RPLP2 to the large 60S subunit. RPLP0 was required for global translation, yet RPLP1 was dispensable while RPLP2 was specifically required for non-canonical poxvirus protein synthesis. Combined, we demonstrate that poxviruses structurally customize ribosomes and become reliant upon traditionally non-essential RPs from both ribosomal subunits for efficient initiation on their late mRNAs.

2024-10-25 | MSV000096224 | MassIVE

Transcriptome and translatome of ribosomal protein-deficient human cells

Project description:Human ribosomes are made of around 80 ribosomal proteins (RPs) and four ribosomal RNAs. To explore gene expression regulation by RPs at the transcriptional and translational levels, parallel RNA-seq and Ribo-seq were conducted in A549 cells after knockdown of individual RP.

2022-01-27 | GSE168445 | GEO

A ribosome assembly stress response regulates transcription to maintain proteome homeostasis

Project description:Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Alteration of any step in this process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. Here we show that arrest of ribosome biogenesis in the budding yeast S. cerevisiae triggers rapid activation of a highly specific stress pathway that coordinately up-regulates Hsf1 target genes and down-regulates RP genes. Activation of Hsf1 target genes requires neo-synthesis of RPs, which accumulate in an insoluble fraction, leading to sequestration of the RP transcriptional activator Ifh1. Our data suggest that levels of newly-synthetized RPs, imported into the nucleus but not yet assembled into ribosomes, work to continuously balance Hsf1 and Ifh1 activity, thus guarding against proteotoxic stress during ribosome assembly.

2019-06-24 | GSE125226 | GEO

Mutant RPL10 prevents large ribosomal subunit maturation

Project description:The eukaryotic ribosome is a complex molecular machine responsible for the translation of mRNA to protein. Faulty ribosome production leads to decreased protein production, increased cellular stress, and often cell death. Previous research on ribosome biogenesis primarily focused on factors facilitating the proper assembly of the ribosome. By contrast, investigations into quality control mechanisms targeting abnormal pre-ribosomes remain relatively unexplored. We established a method to impede the maturation of a small subset of ribosomes in human cells. The assembly of the 60S large ribosomal subunit begins in the nucleolus, continues through the nucleoplasm, and concludes in the cytoplasm with the incorporation of the ribosomal protein uL16/RPL10 and the release of the late-acting biogenesis factors. We designed a system where incorporation of a mutant uL16 lacking residues 102-111 blocks the assembly of the maturing large subunit. To confirm that uL16mut incorporation blocks 60S maturation, we purified tagged uL16wt or uL16mut and identified associated proteins via western blotting and mass spectrometry analysis. We did not detect an interaction between uL16mut-containing large and subunits small subunit proteins, validating that the 60Smut subunits are trapped during biogenesis and unable to pair with small subunits to engage in active translation. We observed significant enrichment of late ribosome biogenesis factors, such as eIF6 and NMD3, upon uL16mut immunoprecipitation.

2025-04-28 | PXD051646 | Pride

Identification of the modifications in artificial E. coli rRNAs

Project description:Ribosome biogenesis is pivotal in the self-replication of life. In Escherichia coli, three ribosomal RNAs and 54 ribosomal proteins are synthesized and subjected to cooperative hierarchical assembly facilitated by numerous accessory factors. Realizing ribosome biogenesis in vitro is a critical milestone for understanding the self-replication of life and creating artificial cells. Despite its importance, this goal has not yet been achieved owing to its complexity. In this study, we report the successful realization of ribosome biogenesis in vitro. Specifically, we developed a highly specific and sensitive reporter assay for the detection of nascent ribosomes. The reporter assay allowed for combinatorial and iterative exploration of reaction conditions for ribosome biogenesis, leading to the simultaneous, autonomous synthesis of both small and large subunits of ribosomes in vitro through transcription, translation, processing, and assembly in a single reaction space. Our achievement represents a crucial advancement toward revealing the fundamental principles underlying the self-replication of life and creating artificial cells.

2024-12-09 | MTBLS7425 | MetaboLights

Ribosomal protein L5 (RPL5/uL18) I60V mutation is associated to increased translation and modulates drug sensitivity in T-cell acute lymphoblastic leukemia cells

Project description:Somatic mutations in ribosomal proteins (RPs), including RPL5, have been reported in approximately 10% of pediatric patients with T-cell acute lymphoblastic leukemia (T-ALL). In cancer, the incorporation of mutant RPs into ribosomes often disrupts canonical ribosome function, thereby contributing to disease development. In this study, we aimed to characterize the effects of the RPL5-I60V mutation in the context of T-ALL, focusing on its impact on translation and cellular responses to a panel of compounds in vitro. Using CRISPR-Cas9, we generated a homozygous knock-in mutant in Jurkat cells and investigated its effects on ribosome biogenesis. We observed both quantitative and qualitative alterations in the production of the large ribosomal subunit. Ribosomes containing the mutant RPL5 protein exhibited intrinsically increased protein synthesis activity, which correlated with enhanced cellular proliferation. We then evaluated the response of these mutant cells to a panel of compounds targeting protein synthesis at various levels—including an MNK1 inhibitor, metformin, silvestrol, homoharringtonine, anisomycin, resveratrol, and hygromycin B—as well as cytarabine, a chemotherapeutic agent commonly used in T-ALL treatment. Our results showed that the RPL5-I60V mutation confers increased sensitivity to most of these compounds, with the exception of hygromycin B. This study advances our understanding of how oncoribosomes contribute to cancer pathogenesis and highlights the therapeutic potential of directly or indirectly targeting altered ribosomes, offering insights for the development of personalized treatment strategies.

2025-11-06 | PXD064727 | Pride

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation

Project description:The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs involves an intricate cascade of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combined biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway highlighting regulatory linkages between different maturation stages. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.

2024-10-17 | PXD046691 | Pride

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