Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The stringent response does not influence ribosome pausing in Bacillus subtilis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE293288 | GEO | 2025/05/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The stringent response does not influence ribosome pausing in Bacillus subtilis [Ribo-Seq]

Project description:The stringent response represses translation and is activated when amino acid levels drop, for example during the stationary phase. Bacillus subtilis, a well-known industrial enzyme production organism, secretes most enzymes during the stationary phase. We were curious whether the stringent response affects ribosome pausing, and whether its absence improves protein production yields in the stationary phase. To investigate this, genome-wide ribosome profiling was used using a stringent response mutant that overexpressed the α-amylase AmyM. Although, blocking the stringent response did increases overall protein synthesis, the secretion of AmyM was actually reduced. The ribosome profiling data revealed that this was not caused by a reduction in translation. In fact, absence of the stringent response did not seem to markedly influence ribosome pausing. However, late in stationary phase an increased ribosome pausing at tryptophane codons emerges, suggesting a depletion of tryptophane. A strong suppression of tryptophane biosynthesis and acquisition genes, under control of the trp RNA-binding attenuation protein TRAP, likely accounts for this, although TRAP does not belong to the stringent response regulon of B. subtilis. Finally, the ribosome profiles revealed several genes with unusually low translation activities, illustrating the importance of translation initiation as a regulatory element of expression.

2025-05-01 | GSE293166 | GEO

The stringent response does not influence ribosome pausing in Bacillus subtilis [RNA-Seq]

2025-05-01 | GSE293165 | GEO

Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis

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

2024-01-01 | GSE250314 | GEO

The stringent response does not influence ribosome pausing in Bacillus subtilis

Project description:The stringent response does not influence ribosome pausing in Bacillus subtilis

| PRJNA1243907 | ENA

Ribosome pausing in amylase producing Bacillus subtilis during long fermentation.

Project description:BackgroundRibosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. In this study, we investigated whether ribosome pausing occurs during production of the α-amylase AmyM by the industrial production organism Bacillus subtilis under repeated batch fermentation conditions.ResultsWe began by assessing our ribosome profiling procedure using the antibiotic mupirocin that blocks translation at isoleucine codons. After achieving single codon resolution for ribosome pausing, we determined the genome wide ribosome pausing sites for B. subtilis at 16 h and 64 h growth under batch fermentation. For the highly expressed α-amylase gene amyM several strong ribosome pausing sites were detected, which remained during the long fermentation despite changes in nutrient availability. These pause sites were neither related to proline or rare codons, nor to secondary protein structures. When surveying the genome, an interesting finding was the presence of strong ribosome pausing sites in several toxins genes. These potential ribosome stall sites may prevent inadvertent activity in the cytosol by means of delayed translation.ConclusionsExpression of the α-amylase gene amyM in B. subtilis is accompanied by several ribosome pausing events. Since these sites can neither be predicted based on codon specificity nor on secondary protein structures, we speculate that secondary mRNA structures are responsible for these translation pausing sites. The detailed information of ribosome pausing sites in amyM provide novel information that can be used in future codon optimization studies aimed at improving the production of this amylase by B. subtilis.

| S-EPMC11770953 | biostudies-literature

Global transcriptional response of Bacillus subtilis to peroxide stress

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

2006-03-07 | GSE4350 | GEO

Bacillus subtilis SigA ChIP-chip

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

2012-01-01 | GSE27652 | GEO

Tracking the elusive function of Bacillus subtilis Hfq

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-22 | E-GEOD-66893 | biostudies-arrayexpress

Tracking the elusive function of Bacillus subtilis Hfq

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