GEO DataSets

(Submitter supplied) The post-transcriptional process of RNA polyadenylation sits at the crossroads of energy metabolism and RNA metabolism. RNA polyadenylation is catalyzed by poly(A) polymerases which use ATP as a substrate to add adenine residues to the 3’ end of RNAs, which can alter their stability. In E. coli, RNA polyadenylation mediated by the major poly(A) polymerase (PAP I) was previously shown to facilitate degradation of individual RNAs. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

24 Samples

Download data: CSV

(Submitter supplied) To investigate the extent of the effect of poly(A) polymerase (PAP I)-mediated polyadenylation on RNA stability, we performed the first genome-wide study of RNA stability in the absence of PAP I activity. Inactivation of the pcnB gene coding for PAP I led to a global stabilization of E. coli RNAs, with 1403 stabilized transcripts and only 4 destabilized. Stabilized RNAs were involved in essential cellular functions such as DNA replication and repair, translation, RNA degradation, central carbon metabolism but also in stress responses. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21726

24 Samples

Download data: CSV

(Submitter supplied) The rate and direction of phenotypic evolution depends on the availability of phenotypic variants induced either genetically or environmentally for selection act upon. Theoretical suggest that genetic interactions between genes governing phenotypes could explain how the bias in phenotypic variability arises. However, it remains unknown whether the phenotypic variability is explained by real known genetic interactions as expected. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18948

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Streptococcus agalactiae; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL28679 GPL29157

26 Samples

Download data

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other

Platforms:

GPL28679 GPL25368

8 Samples

Download data: XLSX

(Submitter supplied) Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via σ32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18956 GPL18133

30 Samples

Download data: TSV

(Submitter supplied) The effectiveness of antibacterial agents is strongly influenced by its antibacterial mechanism, which, in turn, is dependent on the agent’s topological structure. In addition to oxidative stress (especially caused by reactive oxygen species), known to be a key mechanism for 2D phosphorene structures, physical penetration of bacterial cell membranes is predicted for violet phosphorene nanosheets. In this study, we demonstrate that violet phosphorus (VP) and its exfoliated product, violet phosphorene nanosheets (VPNS), have superior antibacterial capability against pathogens.A series of antibacterial tests and theoretical calculations show that VPNS can inactivate >99.9% of two common pathogens (Escherichia coli and Staphylococcus aureus) and >99% of two “superbugs” (i.e., antibiotic-resistant bacteria, Escherichia coli pUC19 and methicillin-resistant Staphylococcus aureus) via oxidative stress combined with cell membrane penetration by VPNS Moreover, VPNS have higher antibacterial activity than black phosphorene nanosheets in vitro and in vivo. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT

(Submitter supplied) Metagenome sequencing enables discovery and genetic characterization of complex microbial communities from diverse ecosystems. However, determining the activity of isolates within a community using transcriptomics presents several challenges including the wide dynamic range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many body sites. To address these limitations, we developed “Targeted Expression Analysis Sequencing” or TEAL-seq. more...

Organism:

Escherichia coli; Staphylococcus aureus; Mus musculus; Staphylococcus epidermidis; Homo sapiens

Type:

Expression profiling by high throughput sequencing

6 related Platforms

129 Samples

Download data: XLSX

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21222

4 Samples

Download data: XLSX

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21222

4 Samples

Download data: XLSX

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) We performed RNA-Seq to accurately assess the impact of AcK addition or biosynthesis on gene expression in E. coli cells.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

9 Samples

Download data: TXT

(Submitter supplied) RNA molecules can populate an ensemble of alternative structural conformations, but the true extent of the RNA secondary structure folding space of a living cell has never been explored. We here generated the first transcriptome-wide maps of RNA secondary structure ensembles in Escherichia coli, both at physiological temperature and upon cold-shock. Our analysis revealed hundreds of novel putative conserved RNA switches.

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL33919 GPL33918

10 Samples

Download data: WIG

(Submitter supplied) Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq). Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

20 Samples

Download data: TSV

(Submitter supplied) The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. more...

Organism:

Salmonella enterica subsp. enterica serovar Heidelberg; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34890 GPL34889 GPL16085

9 Samples

Download data: TXT

(Submitter supplied) L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

48 Samples

Download data: TXT

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21222

8 Samples

Download data: XLSX

(Submitter supplied) RNA mutations are known to change mobility in native gels. What is not known is if mobility can serve as an effective tool to separate structurally similar (structural homologs) from structurally destabilized variants in a deep-mutation library of an RNA. Here we defined the proportion of a mutant in the native band from native polyacrylamide gel electrophoresis (PAGE) as a native-mobility-fitness score. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

16 Samples

Download data: TXT

(Submitter supplied) Bacteria utilize sophisticated mechanisms to detect and adapt to challenging environmental conditions by activating specific genes that help counteract stressors. Over 150 small proteins (≤ 50 amino acids long) are documented in Escherichia coli, but only a fraction of them are well-studied. Many of these proteins do not have an associated phenotype and their biological roles remain elusive. Here, we investigate small proteins induced in response to magnesium limitation using ribosome profiling, RNA sequencing, and transcriptional reporter assays. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21433

6 Samples

Download data: CSV