Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Post-transcriptional Modifications in Two Large Subunit Intermediates Populated in E.coli Cells Expressing Helicase Inactive R331A DbpA

ABSTRACT: RNA Post-transcriptional Modifications in Two Large Subunit Intermediates Populated in E.coli Cells Expressing Helicase Inactive R331A DbpA

PROVIDER: PRJNA807363 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18044700_1.fastq.gz	Fastqsanger.gz
	SRR18044700_2.fastq.gz	Fastqsanger.gz
	SRR18044701_1.fastq.gz	Fastqsanger.gz
	SRR18044701_2.fastq.gz	Fastqsanger.gz
	SRR18044702_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

RNA Post-transcriptional Modifications in Two Large Subunit Intermediates Populated in E.coli Cells Expressing Helicase Inactive R331A DbpA

Project description:23S ribosomal RNA (rRNA) of Escherichia coli 50S large ribosome subunit contains 26 post-transcriptionally modified nucleosides. Here, we determine the extent of modifications in the 35S and 45S large subunit intermediates, accumulating in cells expressing the helicase inactive DbpA protein, R331A, and the native 50S large subunit. The modifications we characterized are nine pseudouridines, 3-methylpseudouridine, 2-methyladenine, and 5-hydroxycytosine. These modifications were detected using 1-cyclohexyl-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate (CMCT) treatment followed by alkaline treatment. In addition, KMnO4 treatment of 23S rRNA was employed to detect 5-hydroxycytosine modification. CMCT and KMnO4 treatment produce chemical changes in modified nucleotides that cause reverse transcriptase misincorporations and deletions, which were detected employing next generation sequencing. Our results show that seven uridines to pseudouridine isomerizations and the 2-methyladenosine modification are present both in the 35S and 45S to similar extents as in the 50S. Hence, the enzymes that perform these modifications, namely RluF, RluB, RlmN, RluA, RluC, and RluA, have already acted in the intermediates. While two uridines to pseudouridines isomerizations, the 3-methylpseudouridine, and 5-hydroxycytosine modifications are significantly less present in the 35S and 45S as compared to the 50S. Therefore, the enzymes that perform these modifications, RluD, RlmH, and RlhA, are in the process of modifying the 35S, and 45S or these enzymes act during the later stages of ribosome assembly. Our study employs a novel high throughput and single nucleotide resolution technique for detection of 2-methyladenine and two novel high throughput and single nucleotide resolution technique for detection of 5-hydroxycytosine.

2022-09-15 | GSE196821 | GEO

RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate

Project description:Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. There are 26 RNA post-transcriptional modifications in 23S RNA of the mature Escherichia coli (E.coli) large ribosomal subunit. The levels of these modifications have been investigated extensively only for a small number of large subunit intermediates and under a limited number of cellular and environmental conditions. In this study we determine the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine, 5-hydroxycytosine and eight pseudouridines in an early-stage E.coli large subunit assembly intermediate with a sedimentation coefficient of 27S. The 27S intermediate is one of three large subunit intermediates accumulated in E.coli cells lacking the DEAD-box RNA helicase DbpA and expressing the helicase inactive R331A DbpA construct. The majority of the investigated modifications are incorporated into the 27S large subunit intermediate to similar levels as in the mature 50S large subunit, indicating that these early modifications or the enzymes that incorporate them have important roles in the initial events of large subunit ribosome assembly.

2024-05-15 | GSE232539 | GEO

Wild type E.coli SE15 vs. LuxS mutant E.coli SE15

Project description:Transcriptional profiling of E.coli SE15 comparing wild type E.coli SE15 with Autoindecur 2 synthesis gene LuxS mutnat E.coli SE15. E.coli SE15 is isolated from indwelling catheter of urinary tract infected patient. Examine change of quorum sensing related gene by deleting autoinducer 2 synthesis gene LuxS in E.coli

2013-08-02 | GSE49474 | GEO

E.coli

Project description:E.coli

| PRJEB11782 | ENA

Analysis of mRNA decay intermediates in Bacillus subtilis 3' exoribonuclease and RNA helicase mutant strains

Project description:Analysis of mRNA decay intermediates in Bacillus subtilis 3' exoribonuclease and RNA helicase mutant strains

| PRJNA792588 | ENA

RNA Post-Transcriptional Modifications in Two Large Subunit Intermediates Populated in <i>E. coli</i> Cells Expressing Helicase Inactive R331A DbpA.

Project description:23S ribosomal RNA (rRNA) of Escherichia coli 50S large ribosome subunit contains 26 post-transcriptionally modified nucleosides. Here, we determine the extent of modifications in the 35S and 45S large subunit intermediates, accumulating in cells expressing the helicase inactive DbpA protein, R331A, and the native 50S large subunit. The modifications we characterized are 3-methylpseudouridine, 2-methyladenine, 5-hydroxycytidine, and nine pseudouridines. These modifications were detected using 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) treatment followed by alkaline treatment. In addition, KMnO4 treatment of 23S rRNA was employed to detect 5-hydroxycytidine modification. CMCT and KMnO4 treatments produce chemical changes in modified nucleotides that cause reverse transcriptase misincorporations and deletions, which were detected employing next-generation sequencing. Our results show that the 2-methyladenine modification and seven uridines to pseudouridine isomerizations are present in both the 35S and 45S to similar extents as in the 50S. Hence, the enzymes that perform these modifications, namely, RluA, RluB, RluC, RluE, RluF, and RlmN, have already acted in the intermediates. Two uridines to pseudouridine isomerizations, the 3-methylpseudouridine and 5-hydroxycytidine modifications, are significantly less present in the 35S and 45S, as compared to the 50S. Therefore, the enzymes that incorporate these modifications, RluD, RlmH, and RlhA, are in the process of modifying the 35S and 45S or will incorporate these modifications during the later stages of ribosome assembly. Our study employs a novel high throughput and single nucleotide resolution technique for the detection of 2-methyladenine and two novel high throughput and single nucleotide resolution techniques for the detection of 5-hydroxycytidine.

| S-EPMC9444345 | biostudies-literature

Comparison of small RNA levels in Dicer helicase mutants

Project description:Years after the discovery that Dicer is a key enzyme in gene-silencing, the role of its helicase domain remains enigmatic. Here we show that this domain is critical for accumulation of certain endogenous small interfering RNAs (endo-siRNAs) in C. elegans. The domain is required for the production of the direct products of Dicer, or primary endo-siRNAs, and consequently, affects levels of downstream intermediates, the secondary endo-siRNAs. Consistent with the role of endo-siRNAs in silencing, their loss correlates with an increase in cognate mRNA levels. We find that the helicase domain of Dicer is not required for microRNA (miRNA) processing, or RNA interference following exposure to exogenous double-stranded RNA. Comparisons of wildtype and helicase-defective strains using deep-sequencing analyses show that the helicase domain is required by a subset of annotated endo-siRNAs, in particular, those associated with the slightly longer 26 nucleotide small RNA species containing a 5M-bM-^@M-^Y guanosine. We reintroduced either wildtype Dicer, or Dicer harboring a mutation (K39A) in it's helicase domain, into dcr-1(ok247) mutant worms via transgene rescue. We then used high-throughput sequencing to compare levels of small RNAs present in each of these strains.

2010-04-01 | E-GEOD-20336 | biostudies-arrayexpress

Bacteria strain:E.coli | isolate:E.coli

Project description:Bacteria strain:E.coli | isolate:E.coli Genome sequencing

| PRJNA1127066 | ENA

Avian E.coli

Project description:Avian E.coli

| PRJEB11955 | ENA

Asta E.coli

Project description:Asta E.coli

| PRJEB18619 | ENA