Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia

ABSTRACT: To gain functional insights into human TSEN/CLP1, we designed an expression vector series based on the MultiBac system that allows combinatorial protein complex production in insect and mammalian cells by utilizing a CMV/p10 dual promoter. Using this system, we were able to assemble and purify functional heterotetrameric TSEN and a heteropentameric complex including the RNA kinase CLP1 from infected insect cells. Individual proteins of the complexes were identified using in-gel digestion and LC-MS/MS analysis. To gain atomistic insights into the molecular architecture of the human TSEN complex, we set out to characterize the TSEN15–34 heterodimer by X-ray crystallography. Despite extensive crystallization trials, full-length TSEN15–34 did not yield any crystals. To define a crystallizable core complex, we subjected the full-length complex to limited proteolysis with subsequent size exclusion chromatography. Primarily, we observed two comigrating polypeptide species. The two polypeptide species were identified using in-gel digestion followed by LC-MS/MS analysis. This led to the identification of the polypeptide species corresponding to residues 23 to 170 of TSEN15 and residues 208 to 310 of TSEN34 covering the predicted conserved nuclease domains.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Marie Alfes

LAB HEAD: Carla Schmidt

PROVIDER: PXD019034 | Pride | 2021-06-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2017_07_05_MB_3.raw	Raw
	2017_07_05_MB_4.raw	Raw
	2017_07_05_MB_5.raw	Raw
	2017_07_05_MB_6.raw	Raw
	2017_07_07_MB_31.raw	Raw

Items per page:

1 - 5 of 25

Similar Datasets

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation Dataset 2A; S. capsularis Y-17639 tRNA-Leu(CAG) deletion Vegetative growth

Project description:In the yeast genera Saccharomycopsis and Ascoidea, nuclear genes use a non-standard genetic code in which CUG codons are translated as serine instead of leucine, due to the presence of a tRNA-Ser with the unusual anticodon CAG. However, some species in this ‘CUG-Ser2’ clade also contain an ancestral tRNA-Leu gene with the same anticodon. One of these species, Ascoidea asiatica, has been shown to have a stochastic proteome in which proteins contain approximately 50% Ser and 50% Leu at CUG codon sites, whereas previously examined Saccharomycopsis species translate CUG only as Ser. Here, we investigated the presence, conservation, and possible functionality of the tRNA-Leu(CAG) gene in the genus Saccharomycopsis. We analyzed the genomes of 33 strains, including almost all known species of Saccharomycopsis, and found that most of them contain both tRNA-Ser(CAG) and tRNA-Leu(CAG) genes. The tRNA-Leu(CAG) gene is evolving faster than tRNA-Ser(CAG) and it has been lost in two species, S. microspora and S. synnaedendra. We deleted the single tRNA-Leu(CAG) gene in S. capsularis and found that it is not essential. Bioinformatic analysis suggested that some CUG codon sites in Saccharomycopsis species may be translated as Leu, specifically in genes with functions in meiosis or sporulation, but mass spectrometry of sporulating S. capsularis and S. fermentans cultures showed only CUG-Ser translation. Cloverleaf structures of tRNA-Leu(CAG) from all Saccharomycopsis species contain mutations that are likely to make them non-functional in translation, but the evolutionary conservation of the gene leads us to propose that it has been retained for an unknown non-translational role.

2024-10-17 | PXD044729 | Pride

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation Dataset 2B; S. capsularis Y-17639 tRNA-Leu(CAG) deletion Sporulation condition

2024-10-17 | PXD044731 | Pride

Unraveling the dataset transcriptomic response of Hydrangea macrophylla stem to mechanical stimulation: de novo assembly and functional annotation

Project description:To gain plant compactness, producers use plant growth regulators (PGRs), in particular growth retardants during culture. However, due to their negative environmental impacts, growth retardants are progressively withdrawn from the market. Alternative, eco-friendly methods such as mechanical stimulation (MS), which mimics the effect imposed on plants by the wind, result in reduced stem elongation, increased stem diameter and increased branching, all of which contribute to plant compactness. So far, few plant species were studied under MS and little is known on molecular response mechanisms to MS. This first transcriptomic data after MS in Hydrangea macrophylla cv. ‘Wudu’® will contribute unravelling how plants respond to mechanical stimuli.

2023-08-01 | GSE238196 | GEO

Genome wide analysis of RNA species present in SMN-containing RNPs

Project description:Several studies indicate that SMN-containing mRNP complexes could be involved in the axonal localization of a large number of mRNAs. We have used murine motor neuron-like NSC-34 cells and RNA Immuno-Precipitation experiments coupled to microarray analyses to perform a genome-wide analysis of RNA species present in mRNP complexes containing the full length SMN protein (flSMN). In situ hybridization and immuno-fluorescence experiments performed on several candidates indicate that these mRNAs colocalize with the SMN protein in neurites and axons of differentiated NSC-34 cells. Moreover, they localize in cell processes in a SMN-dependent manner. Thus, low SMN levels might result in localization deficiencies of mRNAs required for axonogenesis. RNA species coimmunoprecipitated with the SMN protein were used for hybridization of Affymetrix microarrays

2013-11-29 | E-GEOD-40197 | biostudies-arrayexpress

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation 5B; S. capsularis CBS5638 Sporulation

2024-10-17 | PXD044772 | Pride

Dong2018 - E2F dynamics in G1 phase

Project description:The length of the G1 phase in the cell cycle shows significant variability in different cell types and tissue types. To gain insights into the control of G1 length, we generated an E2F activity reporter that captures free E2F activity after dissociation from Rb sequestration and followed its kinetics of activation at the single-cell level, in real time. Our results demonstrate that its activity is precisely coordinated with S phase progression. Quantitative analysis indicates that there is a pre-S phase delay between E2F transcriptional dynamic and activity dynamics. This delay is variable among different cell types and is strongly modulated by the cyclin D/CDK4/6 complex activity through Rb phosphorylation. Our findings suggest that the main function of this complex is to regulate the appropriate timing of G1 length.

2018-11-07 | MODEL1811050001 | BioModels

Dong2018 - E2F dynamics in G1 phase

2018-11-07 | MODEL1811050001 | BioModels

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation Dataset 4B; S. capsularis CBS5064 Sporulation

2024-10-17 | PXD044742 | Pride

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation 4A; S. capsularis CBS5064 Vegetative growth

2024-10-17 | PXD044788 | Pride

tRNA-Leu(CAG) gene is conserved in most Saccharomycopsis yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation Dataset 6B; S. capsularis CBS7262 Sporulation

2024-10-17 | PXD044786 | Pride