Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SutA is a Transcription Elongation Factor Expressed During Slow Growth in Pseudomonas aeruginosa

ABSTRACT: SutA is a Transcription Elongation Factor Expressed During Slow Growth in *Pseudomonas aeruginosa*

PROVIDER: PRJNA276067 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1813200.fastq.gz	Fastqsanger.gz
	SRR1813210.fastq.gz	Fastqsanger.gz
	SRR1813220.fastq.gz	Fastqsanger.gz
	SRR1813201.fastq.gz	Fastqsanger.gz
	SRR1813211.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 21

Similar Datasets

SutA is a Transcription Elongation Factor Expressed During Slow Growth in *Pseudomonas aeruginosa*

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-06-01 | GSE66181 | GEO

SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.

Project description:Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this issue, we used a time-selective proteome-labeling method [bioorthogonal noncanonical amino acid tagging (BONCAT)] to identify proteins synthesized preferentially, but at extremely low rates, under anaerobic survival conditions by the opportunistic pathogen Pseudomonas aeruginosa. One of these proteins is a transcriptional regulator that has no homology to any characterized protein domains and is posttranscriptionally up-regulated during survival and slow growth. This small, acidic protein associates with RNA polymerase, and chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing suggests that the protein associates with genomic DNA through this interaction. ChIP signal is found both in promoter regions and throughout the coding sequences of many genes and is particularly enriched at ribosomal protein genes and in the promoter regions of rRNA genes. Deletion of the gene encoding this protein affects expression of these and many other genes and impacts biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. On the basis of these observations, we have designated the protein SutA (survival under transitions A).

| S-EPMC4747698 | biostudies-literature

Reverse evolution of slow growth

Project description:Compensatory evolution of Pseudomonas aeruginosa slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis

| PRJEB38310 | ENA

Gene expression in P. aeruginosa cystic fibrosis isolates grown on Nematode Growth Medium

Project description:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Existing experimental data in our lab showed significantly different levels of virulence of "early" and "late" P. aeruginosa infection isolates in a C. elegans slow killing model. We wished to examine the expression profile of these isolates in order to explore genes that may be responsible for the observed differences. The expression profiles of two pairs of isolates (four isolates in total) were compared to each other using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating virulence in these isolates. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization

2011-12-31 | GSE33275 | GEO

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [4sURDB-Seq]

Project description:The rate of RNA Polymerase II (RNAPII) elongation has an important role in the control of Alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked-in for a slow elongating form of RNAPII. We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice and impairs the differentiation of ESCs into the neural lineage. This is accompanied by changes in splicing and in gene expression in ESCs and along the pathway of neuronal differentiation. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is more predominant in ESC-differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.

2019-04-15 | GSE127740 | GEO

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [RNA-seq]

2019-04-15 | GSE125413 | GEO

Gene expression in P. aeruginosa cystic fibrosis isolates grown on Nematode Growth Medium

2011-12-31 | E-GEOD-33275 | biostudies-arrayexpress

Synthetic lethality/slow growth with acs2-Ts8

Project description:Obtain synthetic lethality/slow growth gene interactors of acs2-Ts8 Keywords: gene mutation

2006-10-01 | GSE4144 | GEO

Long non-coding RNAs expressed in fast gycolytic and slow oxidative myofibers

Project description:Long non-coding RNAs expressed in fast gycolytic and slow oxidative myofibers

| PRJNA448779 | ENA

Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells

Project description:In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration. We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.

2016-02-09 | E-GEOD-46613 | biostudies-arrayexpress

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