Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stay or Go: Sulfolobales Biofilm Dispersal is Dependent on a Bifunctional VapB Antitoxin

ABSTRACT: A Type II VapB14 Antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius, not only through traditional Toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC Toxins are ribonucleases that are neutralized by their proteinaceous cognate Type II VapB Antitoxin. VapB Antitoxins have a flexible tail at their C-terminus that covers the Toxin’s active site neutralizing its activity. VapB Antitoxins also have a DNA binding domain at their N-terminus that allows them to not only auto-repress their own promoters but also distal targets. VapB14 Antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate Toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for Type II Antitoxins that are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both up-regulated in biofilm cells, supporting the role of the Antitoxin in biofilm regulation. The findings here suggest that a stand-alone VapB-type Antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior.

ORGANISM(S): Sulfolobus acidocaldarius Sulfolobus acidocaldarius DSM 639

PROVIDER: GSE226483 | GEO | 2023/03/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression profile for higA mutant of Pseudomonas aeruginosa PA14

Project description:The previously uncharacterized proteins HigB (unannotated) and HigA (PA4674) of Pseudomonas aeruginosa PA14 were found to form a type II TA system in which antitoxin HigA masks the RNase activity of toxin HigB through direct binding. To determine the physiological role of HigB/HigA in P. aeruginosa, a whole-transcriptome experiment was performed for the higA antitoxin deletion mutant of the PA14 strain compared to the wild-type PA14 strain. The rationale was that for the strain that lacks the antitoxin, the effect of the toxin could be discerned due to enhanced activity of the toxin. Furthermore, toxin HigB reduces production of the virulence factors pyochelin, pyocyanin, swarming, and biofilm formation.

2016-11-04 | GSE74730 | GEO

Transcription profiling of E. coli MqsR and MqsA whole DNA microarray and nickel DNA enrichment microarray

Project description:Here evidence is presented that MqsR and B3021 are a novel toxin-antitoxin (TA) system related to biofilm development and quorum sensing. Using whole-transcriptome studies and nickel enrichment DNA binding microarrays coupled with cell survival studies in which MqsR was overexpressed in isogenic mutants, we identified seven genes involved in MqsR toxicity (clpX, clpP, yfjZ, cspD, relB, relE, and hokA). Quantitative real-time polymerase chain reaction (qRT-PCR) confirmed consistent induction of the seven genes by the overexpression of MqsR as well as induction of nutrient starvation related genes (cstA, rpoS, and dps). Taken together, our results indicate that MqsR toxicity is caused via CspD (a DNA replication inhibitor), other TA systems (RelE/RelB and YfjZ), HokA (a small membrane toxin peptide), and nutrient-starvation conditions induced via CstA, RpoS, and Dps. Additionally, in vivo binding results show antitoxin B3021 binds to the promoter regions of genes encoding essential proteins for stress, growth and normal physiology. Experiment Overall Design: Strain: E. coli K-12 BW25113 wt and mqsR deleted mutant Experiment Overall Design: Medium: LB medium Experiment Overall Design: Temperature: 37 oC Experiment Overall Design: Time: 24 h Experiment Overall Design: Cell type: Biofilm grown on glass wool and planktonic culture

2009-12-05 | E-GEOD-14203 | biostudies-arrayexpress

Transcriptional Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure

Project description:To study the cellular global response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius upon solvent exposure we performed transcriptome comparing the response of planktonic and biofilm cells in absence and presence 1-butanol. S. acidocaldarius was grown in Petri dishes (static incubation) in the absence and presence of 0.5% and 1% (v/v) 1-butanol at 76°C for four days. Planktonic and biofilm cells were harvested and the transcriptional response towards 1-butanol was analysed via RNA-seq. In detail:Biofilm and planktonic cell samples (supernatant after static incubation) were generated in Petri dishes (92 x 16 mm, Polystyrene, without cams, Sarstedt) as described before. Cells grown under six different conditions, including Biofilm-Control (BF0), Biofilm-0.5% (v/v) 1-Butanol (BF05), Biofilm-1% (v/v) 1-Butanol (BF1), Planktonic-Control (PL0), Planktonic-0.5% (v/v) 1-Butanol (PL05), Planktonic-1% (v/v) 1-Butanol (PL1), were seperated, harvested by centrifugation (10 min, 5,000 x g, 4 °C) and immediately frozen at -70 °C. Isolation of cells was performed in triplicates with ten technical replicas each. Samples were pooled to obtain sufficient cell mass for further processing. RNA was isolated using Trizol (Thermo Fisher Scientific). In accordance, sequencing libraries were prepared via Illumina TruSeq stranded mRNA using Ribozero for RNA depletion. Sequencing was performed on a MiSeq instrument (Illumina, San Diego, California, USA) using v3 chemistry with a read length of 2x76 nt.

2021-02-20 | E-MTAB-10093 | biostudies-arrayexpress

Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library

Project description:Protein-protein interaction specificity is often accomplished by molecular recognition and mediated by a small set of interfacial residues. However, the extent to which these residues serve positive specificity roles (encourage interaction with the cognate protein) or negative specificity roles (destabilize interaction with the non-cognate protein) is poorly understood. To systematically dissect these roles, we built a library of interface variants using a bacterial toxin-antitoxin system, Mesorhizobium opportunistum ParD3-ParE3, as a model. The ParD3 antitoxin is specific for its cognate toxin ParE3 and does not neutralize the non-cognate toxin ParE2. We built a saturation mutagenesis library at three key interface positions in ParD3 and measured the ability of each variant to neutralize ParE3 and ParE2 via a 10-hour bulk selection assay. A fitness score was assigned to each variant in the presence of each toxin based on the relative expansion of the variant during the experiment (between t = 0 and t = 600 min).

2020-08-17 | GSE153897 | GEO

Transcription profiling of E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development

Project description:The role of six toxin-antitoxin (TA) systems on biofilm development was investigated (MazEF, RelBEF, ChpB, YefM-YoeB, DinJ-YafQ, and TomB-Hha). Although these TA systems were reported previously to not impact bacterial fitness, we found that biofilm formation is decreased by toxins and increased by anti-toxins, in part, through YjgK. Hence, one role of TA systems is to regulate biofilm formation. Experiment Overall Design: Strains: E. coli K-12 BW25113 wild-type and E. coli BW25113 yjgK deleted mutant Experiment Overall Design: Medium: LB Experiment Overall Design: Cells: biofilm cells on glass wool Experiment Overall Design: Time: 8 h Experiment Overall Design: Temperature: 37oC

2009-02-09 | E-GEOD-12701 | biostudies-arrayexpress

Comparison between E. coli K-12 MG1655 and E. coli K-12 LVM100 delta 5 TA mutant on biofilm cell development

2009-01-28 | GSE11932 | GEO

Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development

2009-01-28 | GSE12701 | GEO

New insights into the regulatory role of the type II antitoxin HigA in Pseudomonas aeruginosa virulence

Project description:Bacterial type II toxin-antitoxin (TA) systems are abundant genetic elements and involved in a diverse array of physiological processes. They encode a protein antitoxin protein that directly binds and effectively neutralizes the protein toxin. Latest studies have highlighted key roles of the type II TA modules in bacterial virulence and pathogenesis but the underlying mechanisms remains elusive. In this study, we investigated the repression function of antitoxin HigA in Pseudomonas aeruginosa infection. Proteomic analysis of the higA deletion strain revealed enhanced expression levels of proteins contributing to pathogenicity. We further verified that HigA negatively controlled T3SS and T6SS expression by directly interacting with the promoter regions of the respective regulators amrZ and exsA. In that sense, relief of HigA-mediated transcriptional inhibition upon stress stimulation could induce virulence genes. These findings reinforce the crucial roles of type II antitoxin in bacterial infection, which highlights the potential of HigBATA system as a target for antibacterial treatment.

2021-05-14 | PXD026084 |

Mechanism of translation inhibition by type II GNAT toxins: AtaT, TacT, and ItaT

Project description:Type II toxin-antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via acetylation of aminoacyl-tRNAs. Using ribosome profiling, we investigated the in vivo substrate specificity of three GNAT toxins: AtaT2, TacT3, and ItaT.

2020-06-17 | GSE148424 | GEO

Role of the PhoP-PhoQ Gene Regulatory System in Adaptation of Yersinia pestis to Environmental Stress in the Flea Digestive Tract

Project description:The Yersinia pestis PhoPQ gene regulatory system is induced during infection of the flea digestive tract and is required to produce adherent biofilm in the foregut, which greatly enhances bacterial transmission during a flea bite. To understand the in vivo context of PhoPQ induction and to determine PhoP-regulated targets in the flea, we undertook whole genome comparative transcriptional profiling of Y. pestis wild-type and ΔphoP strains isolated from infected fleas and from temperature-matched in vitro planktonic and flowcell biofilm cultures. In the absence of PhoP regulation, the gene expression program indicated that the bacteria experience diverse physiological stresses and are in a metabolically less active state. Multiple stress response genes, including several toxin-antitoxin loci and YhcN family genes responsible for increased acid tolerance, were upregulated in the phoP mutant during flea infection. The data imply that PhoPQ is induced by low pH in the flea gut, and that PhoP modulates physiologic adaptation to acid and other stresses encountered during infection of the flea. This adaptive response, together with PhoP-dependent modification of the bacterial outer surface that includes repression of pH 6 antigen fimbriae, supports stable biofilm development in the flea foregut.

2017-02-09 | GSE61558 | 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