Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exploring a Novel Class of Flavoenzymes: Identification and Biochemical Characterization of Ribosomal RNA Dihydrouridine Synthase

ABSTRACT: New Ribosomal RNA Dihydrouridine Synthase in E.coli

PROVIDER: PRJEB77571 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR13362100.fastq.gz	Fastqsanger.gz
	ERR13362101.fastq.gz	Fastqsanger.gz
	ERR13362102.fastq.gz	Fastqsanger.gz
	ERR13362103.fastq.gz	Fastqsanger.gz
	ERR13362104.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 15

Similar Datasets

Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase.

Project description:Dihydrouridine (D), a prevalent and evolutionarily conserved base in the transcriptome, primarily resides in tRNAs and, to a lesser extent, in mRNAs. Notably, this modification is found at position 2449 in the Escherichia coli 23S rRNA, strategically positioned near the ribosome's peptidyl transferase site. Despite the prior identification, in E. coli genome, of three dihydrouridine synthases (DUS), a set of NADPH and FMN-dependent enzymes known for introducing D in tRNAs and mRNAs, characterization of the enzyme responsible for D2449 deposition has remained elusive. This study introduces a rapid method for detecting D in rRNA, involving reverse transcriptase-blockage at the rhodamine-labeled D2449 site, followed by PCR amplification (RhoRT-PCR). Through analysis of rRNA from diverse E. coli strains, harboring chromosomal or single-gene deletions, we pinpoint the yhiN gene as the ribosomal dihydrouridine synthase, now designated as RdsA. Biochemical characterizations uncovered RdsA as a unique class of flavoenzymes, dependent on FAD and NADH, with a complex structural topology. In vitro assays demonstrated that RdsA dihydrouridylates a short rRNA transcript mimicking the local structure of the peptidyl transferase site. This suggests an early introduction of this modification before ribosome assembly. Phylogenetic studies unveiled the widespread distribution of the yhiN gene in the bacterial kingdom, emphasizing the conservation of rRNA dihydrouridylation. In a broader context, these findings underscore nature's preference for utilizing reduced flavin in the reduction of uridines and their derivatives.

| S-EPMC11317573 | biostudies-literature

tRNA binding and modification by the Escherichia coli dihydrouridine synthase DusA

Project description:tRNA binding and modification by the Escherichia coli dihydrouridine synthase DusA

| PRJNA1302775 | ENA

tRNA binding and modification by the Escherichia coli dihydrouridine synthase DusA

Project description:Dihydrouridine (D) is one of the most highly conserved tRNA modifications throughout all domains of life. D20 is particularly conserved and is formed by DusA in E. coli, but its mechanisms and functions remain uncovered. Here, we characterized the molecular mechanisms of DusA in tRNA binding, cofactor oxidation, and tRNA modification, in addition to the cellular functions of DusA in tRNA maturation and mRNA translation. Thereby, we reveal DusA binds tRNA using a two-step mechanism involving local tRNA conformational changes. Although DusA can modify an unmodified tRNA substrate, it binds to previously modified tRNA with a higher affinity. In contrast to the well-studied T arm modifying enzymes TrmA and TruB, DusA does not globally increase tRNA aminoacylation levels, but does improve aminoacylation for specific tRNA species. Despite only few changes in tRNA charging, DusA improves the translation for several specific codons, suggesting a direct role for dihydrouridine in tRNA function on the ribosome. Thus, we propose DusA functions non-redundantly with TrmA and TruB to fine-tune protein synthesis.

2025-09-01 | GSE304803 | GEO

RNA-mediated activity-based protein profiling reveals the substrates of a human dihydrouridine synthase

Project description:RNA-mediated activity-based protein profiling reveals the substrates of a human dihydrouridine synthase

| PRJNA733999 | ENA

Transcriptome-wide mapping of dihydrouridine sites with D-seq

Project description:We report the development of D-Seq, a sequencing based technique for identification of dihydrouridine (D) modifications within RNA. We performed D-Seq on S. cerevisiae and find the first evidence for dihydrouridylation of endogenous mRNAs.

2022-04-16 | GSE175549 | GEO

RNA-mediated activity-based protein profiling reveals dihydrouridine modification on human mRNA

Project description:Epitranscriptomic RNA modifications can regulate RNA activity, however there remains a major gap in our understanding of the scope of mRNA chemistry present in biological systems. Here, we develop RNA-mediated activity-based protein profiling (RNABPP), a chemoproteomic strategy relying upon metabolic RNA labeling with the mechanism-based inhibitor 5-fluorocytidine, mRNA interactome capture, and quantitative proteomics, to investigate pyrimidine-modifying enzymes in human cells. In addition to profiling 5-methylcytidine (m5C) methyltransferase activity on mRNA, metabolic deamination of 5-fluorocytidine to 5-fluorouridine allowed us to show that 5-methyluridine (m5U) is present on human mRNA and demonstrate that its formation is primarily mediated by the tRNA-modifying enzyme TRMT2A. Further, our approach uncovered DUS3L, the mammalian homolog of the yeast tRNA-dihydrouridine synthase DUS3, as a novel 5-fluoropyrimidine-reactive protein. We investigate the mechanism of protein-RNA crosslinking, which involves the conserved catalytic Cys residue, and use genetic knockdown combined with quantitative LC-MS/MS analysis to establish that DUS3L installs dihydrouridine (DHU) on human mRNA and small RNA. Finally, we find that DUS3L is important for cell proliferation and protein translation. Taken together, our work provides a general approach for profiling RNA modifying enzyme activity in vivo, and reveals the existence of new pathways for the epitranscriptomic regulation of mRNA behavior in human cells.

2021-07-16 | PXD022645 | Pride

Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

Project description:Colorectal cancer (CRC) with high rate of mortality is one of the most commonly diagnosed cancers in worldwide. Advanced colorectal cancer is often accompanied by malignant proliferation of tumor cells. Further researches on colorectal cancer proliferation to find new targets and develop new therapeutic regimen are an important direction for colorectal cancer treatment. In this study, genome-wide RNAi screening was used to discover the essential genes associated with colorectal cancer cell proliferation. We found DKC1 (dyskerin pseudouridine synthase 1) promoted CRC proliferation through binding and modifying ribosomal proteins (RPL10A, RPL22L1, RPL34, RPS3) mRNA to increase the mRNAs stability and eventually increasing their expression. Besides, DKC1 is highly expressed in colorectal cancer and its aberrantly high expression is associated with poor prognosis of colorectal cancer patients. These results suggest that DKC1 could be a new therapeutic target for colorectal cancer.

2021-04-30 | GSE147348 | GEO

Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

Project description:Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

| PRJNA613928 | ENA

Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance

Project description:The MHC class I antigen presentation system enables T cell immunosurveillance of cancers and viruses. Rapidly degraded nascent polypeptides (DRiPs) provide many class I peptide ligands. By knocking down each of the 80 ribosomal proteins, we identified proteins that modulate peptide generation without altering source protein expression. We show that 60S ribosomal proteins L6 (RPL6) and RPL28, which are adjacent on the ribosome, play opposite roles in generating an influenza A virus encoded peptide. RPL6 depletion decreases ubiquitin-dependent peptide presentation, while RPL28 depletion increases ubiquitin-dependent and -independent peptide presentation. 40S ribosomal protein S28 (RPS28) knockdown increases total peptide supply in uninfected cells by increasing DRiP synthesis from non-canonical translation of “untranslated” regions and non-AUG start codons, and sensitizes tumor cells for T cell targeting. RPL23 knocKDut decreases overall peptide supply, impairing T cell recognition of tumor cells. Our findings raise the possibility of modulating immunosurveillance by pharmacologically targeting ribosomes.

2019-01-21 | GSE114484 | GEO

From bacterial to human dihydrouridine synthase: automated structure determination.

Project description:The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1-340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain-domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

| S-EPMC4498606 | biostudies-literature

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