Ontology highlight
ABSTRACT:
PROVIDER: PRJNA971182 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:C-di-AMP is primarily associated with the regulation of carbon utilization as well as other central traits, central metabolism, and bacterial stringent response to environmental changes. Elevated c-di-AMP levels result in aberrant physiology for most c-di-AMP synthesizing organisms, drawing particular attention to the importance of the c-di-AMP homeostasis and the molecular mechanisms pertaining to nucleotide metabolism and signal transduction. Here we show that c-di-AMP binds the GntR-family regulator DasR, uncovering a direct link between c-di-AMP and GlcNAc signaling. Further, we show c-di-AMP functions as an allosteric activator of DasR activity. GlcNAc is necessary for cell-surface structure from bacteria to humans, as well as a signal for bacterial development and antibiotic production. DasR is a global repressor that oversees GlcNAc metabolism and antibiotic production, which enables Actinobacteria to cope with stress and starvation. Our in vivo studies reveal the important biological role of allosteric regulation by c-di-AMP in metabolic imbalance and the transduction of a series of signals. Notably, DasR also controls intracellular c-di-AMP level through direct repression on disA. Overall, we identify a function of allosteric regulation between c-di-AMP and DasR in global signal integration and c-di-AMP homeostasis in bacteria, which is likely widespread in Actinobacteria.
2024-03-31 | GSE229938 | GEO
Project description:Deep-sequencing of the engineered production genes in five E coli production chassis strains (BL21(DE3), MG1655, TOP10, W and W3110) producing two case metabolic products, 2,3-butanediol and mevalonic acid
2020-11-17 | E-MTAB-9800 | biostudies-arrayexpress
Project description:The increasing resistence and/or bacterial tolerance to bactericides, such as chlorhexidine, causes worrisome public health problems. Using transcriptomical and microbiological studies, we analysed the molecular mechanisms associated with the adaptation to chlorhexidine in two carbapenemase-producing strains of Klebsiella pneumoniae belonging ST258-KPC3 and ST846-OXA48.
2020-03-21 | GSE147316 | GEO
Project description:High throughput sequencing was used to investigate the production of small RNAs from in Chlamydomonas in different strains and different stages of the life cycle. The association between these and methylation was assessed using genomic sequencing, comparing a sequenced genome with one enriched for methylated DNA sequence by immuno-precipitation. Examination of small RNA production in several strains and of the methylation of regions producing these small RNAs.
2012-08-02 | E-GEOD-23379 | biostudies-arrayexpress
Project description:To investigate gene expression differences of different tylosin high-producing strains, transcriptomes of three tylosin high-producing engineered strains (TLPH08-2, TLPH11 and TLPH17) and the vector control strain TLSET152 were analyzed by RNA-Seq. Different strains (TLSET152, TLPH08-2, TLPH11 and TLPH17) were harvested at 96 h of fermentationat and then RNA isolation, transcriptome sequencing and data analysis were conducted.
2023-08-08 | GSE228908 | GEO
Project description:Responses of Escherichia coli DH5alpha as they overexpress pUC at different ODs in LB + Amp Escherichia coli DH5alpha expressing pUC sampled at different ODs (0.2, 0.5, 0.9) in LB + Amp vs cells not producing pUC
2010-07-01 | E-GEOD-4379 | biostudies-arrayexpress
Project description:Recent whole-genome sequencing of large populations of the same bacterial species has revealed significant disparity among genes in the frequency of single nucleotide polymorphisms (SNPs). For example, a previous analysis of invasive serotype M3 group A streptococci (GAS) found the highest frequency of SNPs in the gene (ropB) encoding the regulator of proteinase B (RopB). This finding led us to hypothesize that RopB polymorphisms contribute to altered GAS host-pathogen interactions. Sequencing of ropB in 171 invasive serotype M3 GAS strains from a surveillance study identified 19 distinct ropB alleles. Inactivation of the ropB gene in strains producing distinct RopB variants had dramatically different effects on GAS global gene expression. Further, analysis of laboratory-generated isoallelic GAS strains differing only by a single amino acid replacement in RopB confirmed that the variant protein affected the transcript level of the gene encoding streptococcal proteinase B, a major RopB-regulated virulence factor. Comparison of parental, RopB-inactivated, and RopB isoallelic strains in mouse infection models demonstrated that RopB polymorphisms significantly influence GAS virulence and disease manifestations. These studies detail a paradigm in which unbiased, whole-genome sequence analysis of populations of clinical bacterial isolates creates new avenues of productive investigation into the pathogenesis of common human infections.
2011-04-01 | GSE26655 | GEO
Project description:Toll/interleukin-1 receptor (TIR) domains across different life kingdoms possess NADase activities and produce distinct small molecules including phosphoribosyl adenosine monophosphate/diphosphate (pRib-AMP/ADP) and two cyclic ADPR (cADPR) isomers 2’cADPR and 3’cADPR. Plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal TIR domain sense pathogen effectors to initiate immune signaling and rely on downstream helper NLRs to execute immune function. Lipase-like proteins EDS1 and PAD4 transduce immune signals from sensor TIR-NLRs to a helper NLR called ADR1. We report the structure and function of Arabidopsis EDS1-PAD4-ADR1 (EPA) heterotrimer in complex with pRib-AMP/ADP activated by plant or bacterial TIR signaling. Bacterial TIRs that produce 2’cADPR, but not 3’cADPR, induce EPA complex formation and activate EPA signaling using pRib-AMP as the signaling molecule. 2’cADPR is hydrolyzed into pRib-AMP in vivo. 2’cADPR, but not 3’cADPR, induces EPA-dependent defense genes expression. Our findings shed light on the activation mechanisms of ADR1 by EDS1-PAD4 involving two structurally-related molecules with 2’cADPR likely being the storage form of the unstable signaling molecule pRib-AMP, as well as cross-talks between plant and bacterial TIR immune signaling.
2025-01-29 | GSE277725 | GEO
Project description:Obtaining an in depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics. Many cationic antimicrobial peptides (AMPs) share a range of structural and physical features that have been linked to antibacterial activity and yet they vary dramatically in their potency towards the same bacterial target. We hypothesised that a whole organism view of AMP challenge on Escherichia coli could provide a sophisticated, bacterial perspective enabling understanding of how potency is linked to mode of action. We used a 1H NMR metabolomic approach to characterise the effect on E. coli of challenge with four structurally and physically related AMPs: magainin 2, pleurocidin, buforin II and a designed peptide comprising D-amino acids only. Sub-inhibitory conditions, where these peptides nevertheless induced a bacterial response, were identified enabling electron microscopic and transcriptomic analyses. Although some common features of the bacterial response to AMP challenge could be identified, the metabolomes, morphological changes and the vast majority of the changes in gene expression were specific to each AMP. We show the antibacterial mode of action of AMPs can be accurately predicted by comparing ontological profiles generated by transcriptomic analyses. The response of E. coli to AMP challenge is highly plastic, with the bacteria capable of deploying a multifaceted response adapted to the mode of action rather than the physical properties of the AMP.
2014-01-21 | E-MTAB-1703 | biostudies-arrayexpress