A global transcription study of the regulatory effects of potassium, glutamate and c-di-AMP in Bacillus subtilis
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PROVIDER: PRJNA658929 | ENA |
REPOSITORIES: ENA
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Project description:Since c-di-AMP has been implicated in the interplay of potassium and glutamate homeostasis, we analysed, using strand-specific tiling arrays (tiling step of 22 nucleotides), global gene expression in the wild type strain B. subtilis 168 at low (0.1 mM) and high (5 mM) potassium concentrations and in the presence of ammonium and glutamate as the nitrogen source as well as in the c-di-AMP free strain (∆disA, ∆cdaA, ∆cdaS) GP2222 and its isogenic suppressor mutant GP2223 that is able to grow at 5 mM potassium. In addition to strongly reduced expression of genes involved in fermentation and respiration (regulated by the NADH-responsive transcription factor Rex), genes of the SigO regulon involved in acid stress response and several competence genes was severely reduced in the mutant strain GP2222. In the wild type strain, the ktrAB and kimA genes were most strongly repressed by potassium. These genes encoding high affinity potassium uptake systems are controlled by a c-di-AMP sensitive riboswitch.Taken together, the analysis confirmed that c-di-AMP is involved in multiple cellular functions including genetic competence and revealed a particular role of genes involved in controlling NADH homeostasis.
2020-12-28 | GSE156738 | GEO
Project description:Cyclic di-AMP is an essential second messenger in many Gram-positive bacteria, including the model organism Bacillus subtilis. Here, we analyzed the transcriptome of a strain accumulating c-di-AMP in vivo. Our results demonstrate that accumulation of c-di-AMP affects the expression of several hundred genes, among them many mother-cell specific sporulation genes. Additionally, the two major biofilm operons, epsA-O and tapA-sipW-tasA, are affected. High levels of c-di-AMP abolish transcription of genes responsible for biofilm formation which in turn leads to a defect in complex colony formation in B. subtilis.
2016-05-25 | GSE79716 | GEO
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:The bacterial second messenger c-di-AMP controls various cellular processes including potassium and osmolyte homeostasis. The c-di-AMP receptor protein DarB of Bacillus subtilis binds to the Rel protein and triggers the Rel-dependent stringent response. Here we report crystal structures of DarB in the ligand-free state and of DarB complexes with c-di-AMP, 3´3´-cGAMP and AMP. DarB consists of two CBS domains and forms a homo-dimer with a parallel, head-to-head assembly of the monomers. The DarB dimer binds two cyclic di-nucleotide molecules or two AMP molecules. Only one adenine of bound c-di-AMP is specifically recognized by DarB, while the second one protrudes out of the donut-shaped protein. This enables DarB to bind also 3´3´-cGAMP, as only the adenine fits to the active site, but not the guanine. In absence of c-di-AMP DarB binds to Rel and stimulates (p)ppGpp synthesis, whereas the presence of c-di-AMP abolishes the interaction. The DarB crystal structures reveal no conformational changes upon c-di-AMP binding, hence, the regulatory function of DarB on Rel must be controlled directly by the bound c-di-AMP. A structural model of the DarB-Rel complex was erived from in silico docking, validated with a mass spectrometric analysis of the chemically cross-linked DarB-Rel complex and mutagenesis studies. Based on the predicted complex structure a mechanism of stringent response regulation by c-di-AMP is suggested.
2022-08-12 | PXD033346 | Pride
Project description:In this study, we showed for the first time that c-di-AMP is produced by C. difficile and controls the uptake of potassium, making it essential for growth. We found that c-di-AMP is involved in biofilm formation, cell wall homeostasis, osmotolerance as well as detergent and bile salt resistance in C. difficile. We identified BusR as a new regulator that binds c-di-AMP and represses the expression of the compatible solute transporter BusAA-AB. Interestingly, a busR mutant is highly resistant to a hyperosmotic or bile salt stress compared to the parental strain while a busAA mutant is more susceptible. A short exposure of C. difficile cells to bile salts resulted in a decrease of the c-di-AMP concentrations reinforcing the hypothesis that changes in membrane characteristics due to variations of the cellular turgor or membrane damages constitute a signal for the adjustment of the intracellular c-di-AMP concentration. In a colonization mouse model, a strain producing elevated c-di-AMP concentrations failed to persist in the gut in contrast to the parental strain. Thus, c-di-AMP is a signaling molecule with pleiotropic effects that controls osmolyte uptake to confer osmotolerance and bile salt resistance in C. difficile and that is important for colonization of the host.
2021-12-27 | GSE192529 | GEO
Project description:Streptococcus pneumoniae harbors two cyclic di-AMP (c-di-AMP) phosphodiesterases Pde1 and Pde2. Previously, we demonstrated that deletion of one or both of these proteins leads to growth retardation in culture media, defects in the bacterial stress response, and attenuation in mouse models of disease. All of these phenotypes are due to increased levels of c-di-AMP, since the nature and break down products of each protein are different, and mutations that lower c-di-AMP levels partially restore growth and stress tolerance in these mutants. However, how c-di-AMP mediates pneumococcal stress resistance and virulence is unknown. To establish how c-di-AMP affects the transcriptome, RNA-Seq analysis was employed to compare gene expression between wild-type and Δpde1Δpde2 (ST2734) pneumococci. Overall, the competence regulon was upregulated in the Δpde1Δpde2 mutant.
2018-04-18 | GSE113231 | GEO
Project description:Second messenger nucleotides such as c-di-AMP are produced by bacteria in response to environmental stimuli and can contribute to the regulation of a number of cellular processes including osmoregulation, envelope homeostasis, central metabolism, and biofilm formation. Here, as part of an effort to uncover the biological significance of c-di-AMP in the opportunistic pathogen Enterococcus faecalis, we utilized high-throughout RNA Sequencing analysis to explore the impact of deletion of genes responsible for c-di-AMP synthesis (cdaA) and degradation (dhhP and gdpP).
2021-05-14 | GSE174381 | GEO
Project description:c-di-GMP and c-di-AMP are important conserved second messenger in bacteria, they play a critical role in a wide range of cellular processes, such as motility, virulence, biofilm formation, cell-cycle progression and cell development, but there are only two c-di-GMP receptors and one c-di-AMP receptors were identified in mycobacteria so far, to identify more c-di-GMP and c-di-AMP receptors we compare the protein expression level of c-di-GMP or c-di-AMP synthesis enzyme overexpression strain with the wild type Mycobacterium smegmatis.
2019-07-03 | PXD010623 | Pride
Project description:Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is uncertain whether specific mechanisms constraint the emergence of resistance. In this study, we first report a conserved role of the signaling nucleotide cyclic-di-AMP in the sensitivity of S. agalactiae to ß-lactam. Specifically, we demonstrate that inactivation of the phosphodiesterase GdpP confers ß-lactam tolerance. Characterizing the signaling pathway revealed an antagonistic regulation by the transcriptional factor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility. Furthermore, we show that simultaneous inhibition of osmolyte transporters activity and transcription by c-di-AMP has an additive effect, sustaining ß-lactam tolerance. Finally, transposon mutagenesis for ß-lactam reduced susceptibility reveals a convergent pattern of mutations, including in the KhpAB small RNA chaperone and the protein S immunomodulator. Overall, our findings suggest mechanisms that may foster antibiotic resistance in S. agalactiae and demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response to cell wall weakening due to ß-lactam activity.
2024-04-25 | GSE262190 | GEO
Project description:Human gingival fibroblasts (HGFs) in the oral cavity are constantly exposed to bacteria and may or may not trigger immune responses. Lately, critical bacterial signaling molecules, cyclic-di-adenosine monophosphate (c-di-AMP) and cyclic-di-guanosine monophosphate (c-di-GMP) which play important roles in immune response to pathogens were discovered. However, response of HGFs to these essential bacterial second messengers has not been fully characterized. As a step towards understanding the response of HGFs to these molecules, we carried out a global proteomics analysis of HGFs treated with either c-di-AMP or c-di-GMP. We found differential expression of several proteins in cyclic dinucleotide (CDN) treated HGFs. Analysis of the differentially expressed proteins showed that interferon signaling proteins such as Interferon-induced GTP-binding protein Mx1 (MX-1), Interferon-induced protein with tetratricopeptide repeats 1 (IFIT-1) and Interferon-induced protein with tetratricopeptide repeats 3 (IFIT-3) were the most significantly upregulated proteins. Functional network analysis showed that 21 biological pathways were significantly regulated by both CDNs while others were differentially regulated. Additionally, the functional analysis also predicted increased proliferation of fibroblast cell lines by c-di-GMP. These findings highlight the critical role played by HGFs in the presence of invading pathogens in the oral mucosa by their activation or inhibition of various molecular pathways.
2021-03-24 | MSV000087090 | MassIVE