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Protemic analysis of the effect of c-di-GMP and c-di-AMP on the protein expression of Mycobacterium smegmatis

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mycobacterium Smegmatis (strain Atcc 700084 / Mc(2)155)

SUBMITTER: Qingbin Hu

LAB HEAD: Zheng-Guo He

PROVIDER: PXD010623 | Pride | 2019-07-03

REPOSITORIES: Pride

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			Action	DRS
	1_1.wiff	Wiff
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Publications

Cyclic di-GMP co-activates the two-component transcriptional regulator DevR in <i>Mycobacterium smegmatis</i> in response to oxidative stress.

Hu Qingbin Q Zhang Jiaxun J Chen Yu Y Hu Lihua L Li Weihui W He Zheng-Guo ZG

The Journal of biological chemistry 20190703 34

Cyclic di-GMP (c-di-GMP) is an important second messenger in bacteria, and its regulatory network has been extensively studied. However, information regarding the activation mechanisms of its receptors remains limited. In this study, we characterized the two-component regulator DevR as a new c-di-GMP receptor and further uncovered a novel co-activation mechanism for effective regulation of DevR in mycobacteria. We show that high c-di-GMP levels induce the expression of the <i>devR</i> operon in ...[more]

PMID: 31270210

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Comparative proteomic analysis of c-di-AMP and c-di-GMP treated human gingival fibroblasts

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

Vibrio vulnificus: normal intracellular c-di-GMP level vs. high intracellular c-di-GMP level

Project description:The profiles of transcripts from the V. vulnificus grown under normal and high c-di-GMP conditions were compared by using a V. vulnificus whole-genome microarray Two-condition experiment, normal c-di-GMP condition vs. high c-di-GMP condition. Biological replicates: 3 control, 3 experimental, independently grown and harvested. One replicate per array. For transcriptome analysis, the V. vulnificus whole genome TwinChip, manufactured and kindly provided by the 21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea), was used.

2013-10-22 | E-GEOD-51459 | biostudies-arrayexpress

Genome-wide maps of gene transcription level of hypoxic Mycobacterium bovis BCG with different c-di-GMP levels

Project description:Objective of the study is to find out how c-di-GMP regulate bacteria under hypoxic conditions and new c-di-GMP receptors.

2021-10-16 | GSE185900 | GEO

Pseudomonas aeruginosa post-translational responses to elevated c-di-GMP levels

Project description:C-di-GMP signaling can directly influence bacterial behavior by affecting the functionality of c-di-GMP-binding proteins. In addition, c-di-GMP can exert an indirect and more global effect on gene transcription or translation, e.g. via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. We induced c-di-GMP production via an ectopically introduced diguanylate cyclase and recorded the transcriptional, translational as well as proteomic profile of the cells. We demonstrate that rising levels of c-di-GMP in P. aeruginosa under growth conditions otherwise characterized by low c-di-GMP levels immediately cause a switch to a non-motile, auto-aggregative phenotype. This switch became apparent before any c-di-GMP-dependent role on transcription, translation, or protein abundance could be observed. Our results indicate that sudden rises in global c-di-GMP pools affect the P. aeruginosa phenotype via an alteration of protein functionality, rather than an impact on global gene transcription or translation.

2024-09-03 | GSE183394 | GEO

Allosteric regulation by c-di-AMP modulates global signal integration in Actinobacteria

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

Gene regulation by elevated c-di-AMP levels in Streptococcus pneumoniae

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

c-di-GMP-induced conformational dynamics of the c-di-GMP-binding protein A (CdbA) from Myxococcus xanthus

Project description:The second messenger c-di-GMP has important functions in response to changing environmental and cellular cues in bacteria. Here, we report the identification of CdbA, a DNA binding protein of the ribbon-helix-helix family in Myxococcus xanthus, and show that it binds c-di-GMP in vitro. CdbA is essential for viability and its depletion caused defects in chromosome organization and segregation resulting in a block in cell division. CdbA binds multiple sites across the M. xanthus genome with moderate sequence specificity; however, its depletion only caused minor changes in transcription. C-di-GMP binding and DNA binding by CdbA are mutually exclusive and substitutions in the CdbA interfaces important for c-di-GMP binding not only abolished c-di-GMP binding but also DNA binding and rendered the mutant proteins non-functional in vivo. Our data are consistent with a model whereby CdbA functions as a nucleoid associated protein to organize the M. xanthus chromosome and the function of CdbA is modulated by c-di-GMP, thus, for the first time, establishing a link between c-di-GMP and chromosome organization and segregation.

2020-04-16 | PXD018028 | Pride

Effect of elevated c-di-GMP in Sinorhizobium meliloti

Project description:Sinorhizobium meliloti is a soil-dwelling symbiotic alphaproteobacterium. Cyclic di-GMP is an important second messenger controlling multiple functions in this microorganism. To understand transcriptional regulation by elevated c-di-GMP in S. meliloti, the transcriptome analysis was performed on the wild type strain S. meliloti Rm2011 carrying either an empty vector pWBT or diguanylate cyclase gene pleD overexpression plasmid pWBT-pleD.

2017-06-01 | E-MTAB-5410 | biostudies-arrayexpress

Vibrio vulnificus: normal intracellular c-di-GMP level vs. high intracellular c-di-GMP level

Project description:The profiles of transcripts from the V. vulnificus grown under normal and high c-di-GMP conditions were compared by using a V. vulnificus whole-genome microarray

2013-10-22 | GSE51459 | GEO

Bacterial c-di-GMP reorganizes hematopoietic stem/progenitors and niches through STING

Project description:Upon systemic bacterial infection, hematopoietic stem and progenitor cells (HSPCs) migrate to the periphery in order to supply a sufficient number of immune cells. Although pathogen-associated molecular patterns (PAMPs) reportedly mediate HSPC activation, how HSPCs detect pathogen invasion in vivo remains elusive. Bacteria use the second messenger bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP) for a variety of activities. Here we report that c-di-GMP comprehensively regulates both HSPCs and their niche cells through an innate immune sensor, STING, thereby inducing entry into the cell cycle and mobilization of HSPCs, while decreasing the number and repopulation capacity of long-term hematopoietic stem cells (LT-HSCs). Furthermore, we show that type I IFN acts as a downstream target of c-di-GMP to inhibit HSPC expansion in the spleen, while TGF-β1 is required for c-di-GMP-dependent splenic HSPC expansion. Our results define novel machinery underlying dynamic regulation of HSPCs and their niches during bacterial infection through c-di-GMP/STING signaling. Ten-week-old mice were intraperitoneally administered PBS or 200 nmol c-di-GMP, and CD150+ CD41- CD48- CD34- Flt3- LSK cells of pooled bone marrow from 10 mice per group were sorted 3 days later. mRNA was then extracted using RNeasy micro (Qiagen). Likewise, CD45- Ter-119- CD31- CD140a+ CD51+ MSCs and CD45- Ter119- CD31+ endothelial cells from c-di-GMP-treated or untreated mice were sorted and mRNA was extracted. cDNA was synthesized from mRNA and hybridized to gene chip Mouse60k (Agilent Technologies) and expression levels analyzed.

2015-02-13 | E-GEOD-65905 | biostudies-arrayexpress

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