TmRNADB
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then examined by immunoprecipitation (IP) enrichment followed by LC-MS/MS analysis. Additionally, RNA-seq differential expression analysis of the mutants compared to the wild-type strain was assessed.
2021-08-09 | E-MTAB-10111 | biostudies-arrayexpress
Project description:We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then examined by immunoprecipitation (IP) enrichment followed by LC-MS/MS analysis.
2021-08-23 | PXD023973 | Pride
Project description:Organisms possessing genetic codes with unassigned codons raise the question of how cellular machinery resolves such codons and how this could impact horizontal gene transfer. Here, we use a genomically recoded Escherichia coli to examine how organisms address translation at unassigned UAG codons, which obstruct propagation of UAG-containing viruses and plasmids. Using mass spectrometry, we show that recoded organisms resolve translation at unassigned UAG codons via near-cognate suppression, dramatic frameshifting from at least -3 to +19 nucleotides, and rescue by ssrA-encoded tmRNA, ArfA, and ArfB. We then demonstrate that deleting tmRNA restores expression of UAG-ending proteins and propagation of UAG-containing viruses and plasmids in the recoded strain, indicating that tmRNA rescue and nascent peptide degradation is the cause of impaired virus and plasmid propagation. The ubiquity of tmRNA homologs suggests that genomic recoding is a promising path to impair horizontal gene transfer and confer genetic isolation in diverse organisms.
2018-09-18 | PXD009643 | Pride
Project description:We assess the mRNA-enrichment performance of a custom-made non-mRNA depletion protocol in comparison to a commercially available mRNA-enrichment kit (Ribo-off, Vazyme). Whereas most available kits focus only on removal of rRNA, our method also targets the transfer-messenger RNA (tmRNA). tmRNA was shown to consume up to 25% of the reads in RNA-sequencing data of Pseudomonas aeruginosa. Our established depletion technique is based on the targeting of overly abundant RNA species (16S and23S rRNA, tmRNA) in total RNA preparations of Pseudomonas aeruginosa PA14 by hybridization with organism-specific DNA probes and subsequent degradation by RNase H treatment. While introducing no systematic bias into the gene expression profile we were able to increase the mRNA read share of the total reads in the samples treated with our mRNA-enrichment protocol to 93% - 99%. Therefore, our custom-made depletion technique outcompeted the commercially available reference kit (72% mRNA share) and represents a cost-efficient mRNA-enrichment method for high-throughput next-generation sequencing.
2020-03-31 | GSE147748 | GEO
Project description:To elucidate whole-transcriptome changes in stationary-phase of growth of L. monocytogenes induced by inactivation of lmo0946 gene, we performed transcriptome comparison of wild-type and its derivative mutant in lmo0946 gene. The analysis revealed very high abundance of two non-coding RNAs, namely Rli47 (sRNA) and SsrA (tmRNA) in both studied strains.
2023-08-05 | E-MTAB-10810 | biostudies-arrayexpress
Project description:In our study, we found that lack of tmRNA affects the biofilm formation in Bacillus subtilis, which has important research significance. Then, we obtained a revertant strain MB from tmRNA mutant strain. And MB strain could restore biofilm production capacity. Therefore, the transcriptomes of the three strains were sequenced. Based on the statistical analysis of gene expression (P < 0.05), there were 756 genes up regulated while 992 genes down regulated by at least two folds when comparing TM to WT. Secondly, there were 974 genes up regulated while 563 genes down regulated by at least two folds when comparing MB to TM. And there were 179 genes up regulated while 307 genes down regulated by at least two folds when comparing MB to WT.
2022-08-03 | GSE199151 | GEO
Project description:Bacterial persisters are a small proportion of phenotypically heterogeneous variants with the transient capability to survive in high concentrations of antibiotics, causing recurrent infections in both human and aquatic animals. Transfer-messenger RNA (tmRNA), which was encoded by the <i>ssrA</i> gene, was identified as a determinant regulator mediating the persistence to β-lactams in the pathogenic <i>Aeromonas veronii</i> C4. The deletion of tmRNA exhibited the increased ability of persister formation most probably due to the reduction of protein synthesis. Transcriptomic and metabolomic analyses revealed that the absence of tmRNA not only significantly elevated the intercellular levels of metabolite GlcNAc and promoted NaCl osmotic tolerance, but also upregulated the expression of metabolic genes in both the upstream biosynthesis pathway and the downstream metabolic flux of peptidoglycan (PG) biosynthesis. Finally, exogenous GlcNAc stimulated significant bacterial growth, enhanced content of GlcNAc in the cell wall, higher resistance to osmotic response, and higher persistence to cefotaxime in a concentration-dependent manner, implying its potential role in promoting the multiple phenotypes observed in tmRNA deletion strains. Taken together, these results hint at a potential mechanism of persister formation mediated by tmRNA against the β-lactam challenges in <i>A. veronii</i>.
2021-10-18 | MTBLS1182 | MetaboLights
Project description:<p>Bacterial persisters refer to a small proportion of phenotypically heterogeneous variants with transient capability for survival when exposing to high concentrations of antibiotic, which constitute the major cause for recurrent infections both in human and aquatic infections. In pathogenic bacteria Aeromonas veronii, tmRNA (transfer-messenger RNA), the core factor of trans-translation system, was identified as a determinant regulator mediating the persistence to β-lactams. Compared with the wild type, the deletion of tmRNA exhibited unchanged growth rate, sustained susceptibility to cefotaxime, but did increase persister cell formation. Transcriptomic and metabolomic analyses revealed that, the absence of tmRNA not only upreglated the expressions of metabolic genes especially in the metabolic flux of peptidoglycan biosynthesis, but also significantly elevated the intercellular level of metabolite GlcNAc, thereby intensifying the contents of peptidoglycans in the cell wall. Eventually, exogenous GlcNAc stimulated significantly the bacterial growth and persistence to cefotaxime in a concentration dependent manner. Taken together, these results uncover a novel mechanism of persister formation mediated by tmRNA against the β-lactam challenges.</p>
2020-01-10 | MTBLS1191 | MetaboLights
Project description:Massive data testing about molecular networking using GNPs website
| MSV000088138 | GNPS