Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosomal Assembly Factor Ltv1_L216S Mass Spec

ABSTRACT: Mass spectrometry data of purified ribosomes in S. cerevisiae containing WT Ltv1 or mutation Ltv1_L216S.

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Ebba Blomqvist

LAB HEAD: Katrin Karbstein

PROVIDER: PXD046239 | Pride | 2023-10-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MS221104_KK_KB.mzid.sf3	Mzid
	MS221104_KK_KB_1_Ltv_1.mzid.gz	Mzid
	MS221104_KK_KB_1_Ltv_1.mzid_MS221104_KK_KB_1_Ltv_1.MGF	Mzid
	MS221104_KK_KB_2_Ltv_1.mzid.gz	Mzid
	MS221104_KK_KB_2_Ltv_1.mzid_MS221104_KK_KB_2_Ltv_1.MGF	Mzid

Items per page:

1 - 5 of 14

Similar Datasets

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

Project description:Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A-H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A-H2B deposition by FACT. 6 samples, 2 inputs and 4 ChIP samples for histone H2B (2 for wild-type and 2 for an H2B â30-37 mutant)

2016-08-10 | E-GEOD-80831 | biostudies-arrayexpress

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5.

Project description: Not available

| S-EPMC6984702 | biostudies-literature

Assembly of the 30S ribosomal subunit: positioning ribosomal protein S13 in the S7 assembly branch.

Project description: Not available

| S-EPMC1370675 | biostudies-literature

Functional analysis of BipA in E. coli reveals the plasticity of 50S ribosome assembly

Project description:BipA is a conserved translational GTPase that resembles elongation factor EF-G and 30S assembly factor LepA. Recent evidence suggests that BipA functions in 50S subunit assembly, but the precise role of the factor remains unclear. Here, we use stable isotope labeling of amino acids in culture and mass spectrometry (SILAC / MS) to examine the function of BipA in ribosome biogenesis. During growth at suboptimal temperature, loss of BipA leads to accumulation of immature large subunit particles (~40S) that lack several proteins. These include L2, L7/12, L10, L14, L16, L17, L19, L27, L28 and L32. Parallel analysis of the control (wild-type) strain shows accumulation of virtually identical intermediate particles, although at much lower levels. Further analysis showed that the main path of 50S assembly differs depending on media in which the cells are grown, demonstrating the robust and flexible nature of the assembly process.

2021-09-09 | PXD017917 | Pride

Ribosome protein composition in wt and 23S+5S rRNA ribosomes

Project description:The 120-nt long 5S rRNA, is an indispensable component of cytoplasmic ribosomes in all living organisms. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether maintaining 5S rRNA as an independent molecule is critical for ribosome function and cell survival. By fusing circularly permutated 5S rRNA (cp5S) with 23S rRNA and deleting all wild type 5S rRNA genes, we generated an Escherichia coli strain completely devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is not required for cell growth at 37°C and is unlikely to have essential functions outside the ribosome. The fully-assembled ribosomes carrying 23S-cp5S hybrid rRNA and lacking free 5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits that are unable to form stable 70S ribosomes. Cryo-EM analysis revealed a dramatically malformed peptidyl transferase center in the misassembled 50S subunits. The results of our experiments argue that the key evolutionary force preserving the autonomous nature of the smallest rRNA is its role in ribosome biogenesis.

2020-06-18 | PXD019058 | Pride

Novel roles for ribosomal histidine methylation revealed by proteomics and large-scale cross-linking mass spectrometry

Project description:The methylation of histidine residues is increasingly found to be both prevalent throughout the proteome, and also relevant to human disease. Hpm1p mono-methylates H243 in the ribosomal protein Rpl3 and represents the only histidine methyltransferase in Saccharomyces cerevisiae. Interestingly, the hpm1 deletion strain is highly pleiotropic, with many extra-ribosomal phenotypes including improved growth rates in alternative carbon sources. Here we aimed to understand how methylation of one histidine in one ribosomal protein could result in such diverse phenotypes by combining targeted mass spectrometry, growth assays, quantitative proteomics and cross-linking mass spectrometry. We confirmed the localisation and stoichiometry of the H243 site, found unreported sensitivities of Δhpm1 yeast to non-ribosomal stressors, and identified thirty differentially-abundant proteins upon hpm1 knockout, most with clear links to the coordination of sugar metabolism. We adapted the emerging technique of quantitative large scale cross-linking mass spectrometry for use in budding yeast, which resulted in the identification of 1,267 unique in vivo lysine-lysine pairs. By reproducibly monitoring over 350, we detected changes to membrane protein structure, chromatin compaction, and mitochondrial protein-protein interactions, independently of changes in protein abundance themselves. Taken together, these studies reveal a clear role for Hpm1p in the coordination of sugar metabolism, contextualise the deletion strain’s pleiotropy and illustrate how cross-linking mass spectrometry can generate mechanistic insights into complex cellular processes.

2022-08-12 | PXD027953 | Pride

Nucleolar TFIIE plays a role in ribosomal biogenesis and performance

Project description:Ribosome biogenesis is a highly energy-demanding process in eukaryotes which requires the concerted action of all three RNA polymerases. In RNA polymerase II transcription, the general transcription factor TFIIH is recruited by TFIIE to the initiation site of protein-coding genes. Distinct mutations in TFIIH and TFIIE give rise to the degenerative disorder trichothiodystrophy (TTD). Here we uncovered an unexpected role of TFIIE in ribosomal RNA synthesis by RNA polymerase I. With high resolution microscopy we detected TFIIE in the nucleolus where TFIIE binds to actively transcribed rDNA. Mutations in TFIIE affects gene-occupancy of RNA polymerase I, rRNA maturation, ribosomal assembly and performance. In consequence, the elevated translational error rate with imbalanced protein synthesis and turnover results in an increase in heat-sensitive proteins. Collectively, mutations in TFIIE – due to impaired ribosomal biogenesis and translational accuracy – lead to a loss of protein homeostasis (proteostasis) which can partly explain the clinical phenotype in TTD.

2021-11-16 | PXD023451 | Pride

YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.

Project description: Not available

| S-EPMC12560758 | biostudies-literature

Yeast background with high-concentration spikes

Project description:Microarray measurements are susceptible to error caused by cross-hybridization and bulk hybridization. To characterize the effect of these off-target interactions, we analyzed samples made from baseline (S. cerevisiae) alone or mixed with a high-concentration 1kb spike. The spike is a 1 kb sequence amplified from the Schizosaccharomyces pombe gene SPAC27D7.10c, with an added oligo(dT)-T7 promoter. The baseline and spike samples were mixed at the double-stranded cDNA stage. Three arrays: 100% baseline, 99% baseline + 1% spike, 90% baseline + 10% spike. There are no replicates.

2010-03-21 | E-GEOD-16980 | biostudies-arrayexpress

A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly.

Project description: Not available

| S-EPMC4016315 | biostudies-literature