Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome of synthetic ribosomal 40S subunit

ABSTRACT: In this study, we present the first methodology (to the best of our knowledge) enabling reconstruction of the eukaryotic 40S ribosome subunit with completely customized r-proteins, referred to as “Ribo-swap” (Figure 1). In Ribo-swap, a designer platform yeast was developed through relocating the 56 genes encoding the whole set of 32 40S r-proteins from native genome loci to a synthetic gene cluster, which could be further swapped by another one encoding customer-designed 40S r-proteins to reconstruct customer 40S ribosome subunits in yeast.

ORGANISM(S): Saccharomyces Cerevisiae

SUBMITTER: Guanghou Zhao

PROVIDER: PXD054321 | iProX | Sat Jul 27 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Prediction of ribosomal elongation rate from ribosome profiling data

Project description:We leverage a model statistical framework coupled with high resoluation ribosome profiling data to produce robust estimates of per-codon elongation rates in yeast.

2018-08-18 | GSE102837 | GEO

Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

Project description:Fe-BABE probing of Upf1 binding site on yeast ribosome

2017-12-06 | GSE104072 | GEO

Puf3 participates in ribosomal biogenesis in malaria parasites

Project description:Recent studies of the Puf family of RNA-binding proteins revealed that besides their traditional roles in translational regulation of mRNAs, some Puf proteins are also involved in ribosome biogenesis by binding rRNA. In this study, we report the role of a Puf-like protein in Plasmodium falciparum (name as PfPuf3) and its ortholog PyPuf3 in Plasmodium yoelii in ribosome biogenesis. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which involved in ribosome biogenesis. Neither pfpuf3 nor pypuf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle (IDC). A time-course study of PfPuf3 protein indicated that PfPuf3 was expressed during the entire IDC, with peak expression in early trophozoites. Cellular fractionation of PfPuf3 revealed that it is preferentially partitioned to the nuclear than the cytoplasmic fractions, which is consistent with a nuclear localization of PfPuf3::GFP and PyPuf3::GFP as seen by immunofluorescence. Further, we found PfPuf3 co-localized with a well-known nucleolus maker, PfNop1, demonstrating that PfPuf3 is a nucleolar protein. This localization is in contrast to the cytoplasmic localization of PfPuf1 and PfPuf2, but matches the localization of human Puf-A and yeast Puf6. Affinity purification of an N-terminal PTP-tagged variant of PfPuf3 revealed an association with 32 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and ITS2. Taken together, these results demonstrate a nucleolar localization of PfPuf3 and suggest an essential function of PfPuf3 in ribosomal biogenesis.

2018-03-11 | GSE105126 | GEO

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Project description:The noncoding genome plays an important role in de novo gene birth and the emergence of genetic novelty. Nevertheless, how the properties of noncoding sequences could promote the birth of novel genes and shape the structural diversity and evolution of proteins remains unclear. Here, we investigated the potential of the noncoding genome of yeast to produce novel protein bricks that can give rise to novel genes or be integrated in pre-existing proteins, thus participating in protein structure evolution and diversity. Combining different bioinformatics approaches, we showed that intergenic ORFs of yeast encompass the large structural diversity of canonical proteins with the majority encoding peptides predicted as foldable. Then, we investigated the early stages of de novo gene birth with Ribosome Profiling and systematic reconstruction of yeast de novo gene ancestral sequences. We highlighted sequence and structural factors determining de novo gene birth and protein evolution. Finally, we showed a strong correlation between the fold potential of de novo genes and their ancestral ORFs reflecting the relationship between the noncoding genome and the protein structure universe.

2021-09-13 | GSE173861 | GEO

NBS1 facilitates pre-ribosomal RNA biogenesis

Project description:Mutations of NBS1 gene result in Nijmegen breakage syndrome (NBS), and the gene encodes NBS1 that forms a complex with MRE11 and RAD50 and participates in DNA damage repair. However, the molecular mechanism by which the mutations of NBS1 cause clinical phenotypes of NBS, such as craniofacial dysmorphism, is still unclear. Here, we show that NBS1 localizes at the rDNA loci in the nucleoli and interacts with ribosome RNA (rRNA) transcription machinery including RNA polymerase I (Pol I) and TCOF1. Loss of NBS1 impairs Pol I-dependent transcription of pre-rRNA and induces nucleolar stress. In particular, lacking Nbs1 in mouse neural crest cells not only leads to the reduction of ribosome biogenesis but also craniofacial abnormalities during prenatal development. Moreover, the C-terminus of NBS1 is associated with pre-rRNA and a number of pre-rRNA processing factors, which may also facilitate pre-rRNA maturation. Taken together, our study reveals the functions of NBS1 in rRNA biogenesis.

2025-02-24 | PXD061157 |

Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [Ribosome Profiling]

Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.

2019-05-20 | GSE126234 | GEO

Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [RNA sequencing]

2019-05-20 | GSE126233 | GEO

CD4+ T cells mRNA profiles of lean and obese mice

Project description:To figure out how obesity drives glycolysis in CD4+ T cells, we performed RNA-sequencing to analyze the transcriptome of lean and obese-derived splenic CD4+ T cells. Mice were fed with either a normal diet (referred to lean mice) or a high-fat diet (HFD, 60 kcal% fat, referred to obese mice) generally from 6-8 weeks of age, for up to 4 months.

2023-01-11 | GSE188864 | GEO

Transcriptional profiling of ribosomal protein knockouts

Project description:Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes, and support the existence of a ribosomal code. Keywords: genetic modification

2007-11-06 | GSE8761 | GEO

Ribosome profiling and mRNA seq demonstrate that insertion of common resistance cassettes in yeast drives aberrant transcription

Project description:Our study found that insertion of commonly used selection cassettes in yeast can drive aberrant transcription events and disrupt expression of neighboring genes. We performed ribosome profiling and mRNA-seq on yeast strains where ORFs had been replaced with common selection cassettes and observed aberrant transcripts. Aberrant transcripts positioned near adjacent genomic loci repressed protein synthesis of those genes by transcription interference (ablating normal length transcript production) coincident with translation of competitive uORFs on the long transcript which prevented translation of the main ORF seen by ribosome profiling.

2022-11-29 | GSE207189 | 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