Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis

ABSTRACT: Phenotypic heterogeneity in bacteria results from stochastic processes or deterministic genetic programs. These deterministic programs often incorporate the versatile second messenger c-di-GMP, and by deploying c-di-GMP metabolizing enzyme(s) asymmetrically during cell division give rise to daughter cells with different c-di-GMP levels. Here, we identify a deterministic c-di-GMP-dependent genetic program that is hardwired into the cell cycle of Myxococcus xanthus to minimize cellular heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity switched on during cytokinesis, resulting in a dramatic but transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating mirror-symmetric, phenotypically similar daughters with correct motility behaviours. These findings suggest a general c-di-GMP-dependent mechanism for minimizing cellular heterogeneity, and demonstrate that bacteria by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations ensure the formation of dissimilar or similar daughter cells.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Myxococcus Xanthus

TISSUE(S): Cell Culture, Blood

SUBMITTER: Timo Glatter

LAB HEAD: Timo Glatter

PROVIDER: PXD049046 | Pride | 2024-02-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DMXA-1_report.tsv	Tabular
	MHDMXA-1-01re.raw	Raw
	MHDMXA-1-02re.raw	Raw
	MHDMXA-1-03re.raw	Raw
	MHDMXA-1-04re.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 and isogenic pdhS2 (Atu1888) deletion strain

Project description:A conserved regulatory pathway directs developmental transitions and asymmetries in Agrobacterium tumefaciens. Core components of this coordination of division and development (CDD) pathway include two integrated phosphorelays. One of these phosphorelays includes at least four histidine sensor kinase homologues, DivJ, PleC, PdhS1, and PdhS2, and at least two response regulators, DivK and PleD. Previously we demonstrated that PdhS2 reciprocally regulates biofilm formation and swimming motility. In the current study we further dissect the architecture of the CDD pathway in A. tumefaciens with respect to PdhS2. We show that PdhS2-dependent effects on attachment and motility require the response regulator, DivK, but do not require PdhS2 autokinase or phosphotransfer activities. We also demonstrate that PdhS2 regulation of biofilm formation is dependent upon multiple diguanylate cyclases, including PleD, DgcA, and DgcB, implying that PdhS2 regulation of this process intersects with pathways regulating levels of the second messenger cyclic-di-GMP. Finally, we show that upon cell division a GFP fusion to PdhS2 dynamically localizes to the new pole of the bacterium suggesting that PdhS2 controls processes in the daughter cell compartment of predivisional cells. These observations suggest that PdhS2 negatively regulates DivK, and possibly PleD, activity to control developmental processes in the daughter cell compartment of predivisional cells, as well as in newly released motile daughter cells. Three biological replicates, independent RNA preparations, one dye swap.

2015-07-24 | E-GEOD-71267 | biostudies-arrayexpress

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

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

Comparative proteomic analysis of exoproteome and membrane enriched fractions of PAK and PAK pJN2133 strains

Project description:This work characterizes a P.aeruginosa strain with low levels of c-di-GMP resultant from the overexpression of the phosphodiesterase PA2133. Phenotypic characterization showed that biofilm formation, adhesion to epitheliel cells, and motility are severely impaired in this strain. We applied both, DIGE / MALDI-TOF/TOF and shotgun LC/MS/MS quantitative proteomic analysis to exoproteome and enriched membrane protein fractions. Results from both complementary strategies were in agreement and revealed motility, type III secretion, and chemotaxis to be the main affected processes by PA2133 overexpression. These results are the first to show that flagella synthesis, twitching motility, and chemotaxis are negatively regulated by low c-di-GMP levels in P.aeruginosa and thus confront our current undertsandings of c-di-GMP signalling.

2017-09-05 | PXD004365 | Pride

A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella

Project description:Flagellum plays a crucial role in the invasion process of Salmonella, while also functioning as a significant antigen to trigger host pyroptosis. The regulation of flagella biogenesis is essential for both pathogenicity and immune escape of Salmonella. Here, we identified the conserved and unknown function protein STM0435 as a new flagellar regulator. ∆stm0435 strain exhibit higher pathogenicity in both cellular and animal infection experiments compared to wild-type Salmonella. Conjoint analysis of proteomics and transcriptomics demonstrated that almost all the ﬂagellar genes were dramatically increased in a ∆stm0435 strain compared to wild-type Salmonella. Microscale thermophoresis assay showed that the purified STM0435 protein bound c-di-GMP with a ~194 µM KD affinity. The crystal structures of apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137 and D138 of STM0435 are essential for c-di-GMP binding. Mutant that is unable to bind to c-di-GMP loses its ability to regulate motility, indicating that STM0435 affected the Salmonella ﬂagellar biogenesis process by binding to c-di-GMP.

2023-08-05 | GSE239303 | GEO

Comparison of Expression Profiles for Agrobacterium tumefaciens visR mutant to wild-type strain.

Project description:Many bacteria colonize surfaces and transition to a sessile mode of growth. The plant pathogen Agrobacterium tumefaciens produces a unipolar polysaccharide (UPP) adhesin at single cell poles that contact surfaces. Here we report that elevated levels of the intracellular signal cyclic diguanosine monophosphate (c-di-GMP) lead to surface-contact-independent UPP production and a red colony phenotype due to production of UPP and the exopolysaccharide cellulose, when A. tumefaciens is incubated with the polysaccharide stain Congo Red. Transposon mutations with elevated Congo Red staining identified presumptive UPP-negative regulators, mutants for which were hyperadherent, producing UPP irrespective of surface contact. Multiple independent mutations were obtained in visN and visR, activators of flagellar motility in A. tumefaciens, now found to inhibit UPP and cellulose production. Expression analysis in a visR mutant and isolation of suppressor mutations, identified three diguanylate cyclases inhibited by VisR. Null mutations for two of these genes decrease attachment and UPP production, but do not alter cellular c-di-GMP levels. However, analysis of catalytic site mutants revealed their GGDEF motifs are required to increase UPP production and surface attachment. Mutations in a specific presumptive c-di-GMP phosphodiesterase also elevate UPP production and attachment, consistent with c-di-GMP activation of surface-dependent adhesin deployment. Three biological replicates, independent RNA preparations, one dye swap.

2014-08-21 | E-GEOD-60565 | biostudies-arrayexpress

Gene expression profiles in TICAM1 knockout and wild-type MEFs

Project description:TICAM1 knockout and wild-type (TICAM1 knockout MEFs with restored TICAM1 expression) MEFs were treated by c-di-GMP or DMSO for 4 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. Changes in gene induction, especially of interferon-stimulated genes, between c-di-GMP and DMSO treated cells were examined. Total RNA from c-di-GMP or DMSO treated wild-type MEFs, c-di-GMP or DMSO treated TICAM1 knockout MEFs were analyzed. Gene expression was compared between c-di-GMP treated and DMSO treated samples.

2016-07-29 | E-GEOD-78205 | biostudies-arrayexpress

The Pleiotropic Effects of c-di-GMP content in Pseudomonas syringae

Project description:Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) plays important roles in various cellular functions including the formation of biofilm in a wide range of bacteria, its function in model plant pathogen Pseudomonas syringae is largely elusive. In order to test this in P. syringae, we overexpressed a diguanylate cyclase (YedQ) and a phosphodiesterase (YhjH) that are originally from Escherichia coli, resulting in high and low c-di-GMP levels in P. syringae, respectively. Through performing genome-wide RNA sequencing of these two strains, we found that c-di-GMP regulates (i) fliN, fliE and flhA genes, which are associated with flagellar assembly, (ii) alg8 and alg44, which are related to exopolysaccaride biosynthesis pathway, (iii) pvdE, pvdP and pvsA genes, related to siderophore biosynthesis pathway, and (iv) sodA, which is a superoxide dismutase. In particular, we identified five genes sensitive to elevated c-di-GMP level and constructed five luciferase-based reporters that effectively respond to intracellular level of c-di-GMP in P. syringae, which can be used to measure c-di-GMP levels in vivo in the future. Based on the RNA-seq results, phenotypic assays confirmed that c-di-GMP regulated many important biological pathways in P. syringae, such as negative regulation of type III secretion system (T3SS) and motility as well as positive regulation of EPS production, siderophore production and oxidative stress resistance. Taken together, the present study demonstrated that c-di-GMP is closely related to virulence and stress response in P. syringae, suggesting that tuning its level can be a new strategy to protect plants from the attack of this pathogen in the future.

2019-03-31 | GSE120889 | GEO

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 and isogenic pdhS2 (Atu1888) deletion strain

2015-07-24 | GSE71267 | GEO

The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP

Project description:The cyanobacterial phytochrome Cph2 is a light-dependent diguanylate cyclase producing the second messenger c-di-GMP. Under blue light, the Cph2-dependent increase in the cellular c-di-GMP concentration leads to inhibition of motility in the cyanobacterium Synechocystis 6803. However, the targets of c-di-GMP in this cyanobacterium and its mechanism of action remained unclear. Here, we determined the cellular concentrations of three cyclic nucleotides in wild-type and Δcph2 cells after blue- and green light illumination. Inactivation of the photoreceptor gene completely abolished the blue-light dependent increase in the c-di-GMP content. Microarray analysis revealed that in the wild type in comparison to the Δcph2 mutant, blue light mainly led to a change in accumulation of mRNAs encoding minor pilins, putative chaperone usher pili as well as several chemotaxis regulators. The mRNA encoding the minor pilins pilA5-pilA6 is negatively affected by high c-di GMP content under blue light, whereas the minor pilin encoding operon pilA9-slr2018 accumulates under the same conditions, suggesting opposing functions of the respective gene sets. Based on mutational and gene expression analysis, we further suggest that the second Synechocystis 6803 homolog of a CRP-like transcription factor, SyCRP2, is the regulator of minor pilin gene expression and of putative chaperone usher pili genes slr1667/slr1668. Thus, our work indicates that the Cph2-mediated increase in cellular c-di-GMP concentration upon blue-light illumination specifically changes the transcriptome of Synechocystis 6803.

2020-03-23 | GSE116409 | GEO

Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes

Project description:Pseudomonas aeruginosa is a Gram-negative bacterium able to survive and adapt in a multitude of niches as well as thriving within many different hosts. This versatility lies within a large genome of ca 6Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widely spread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. It is made by diguanylate cyclases and broken by phosphodiesterases while the intracellular level of this molecule drives phenotypic responses. The signaling involve modification of enzymes or proteins function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca 40 genes encoding putative DGC or PDE. The combined activity of those enzymes should reflect the c-di-GMP concentration while specific phenotypic output could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool, with essentially an impact on biofilm phenotypes including initial attachment and maturation, while very little is observed on motility which differs from previous studies. We observe that minor changes in c-di-GMP level have a drastic phenotypic impact thus supporting the idea of local vs global c-di-GMP pool. Our RNA-seq analysis indicates that all PAO1 dgc/pde genes are expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks owe to be reconstructed in one single strain and cannot be built by cross-comparison with studies in other strains.

2022-05-23 | GSE203348 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data