Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacteroidota assemble a unique type VI secretion system membrane complex

ABSTRACT: Microbes have evolved elaborate mechanisms to cope with competitors, including the type VIsecretion system (T6SS) of Gram-negative bacteria. The T6SS inhibits target cells through contact-dependent translocation of toxic effector proteins across two cellular membranes via an inverted phage-like apparatus. Proteobacteria accomplish this feat by passage of theT6SS needle through a megadalton-size membrane complex (MC), which is essential for T6SS function. Remarkably, although the phylum Bacteroidota encodes a T6SS, it lacks homologs of the MC. We identified five novel genes, essential for T6SS function, that encode a candidate unique Bacteroidota T6SSMC. We purified the T6SSiii MC and revealed its dimensions using electron microscopy. We identified an intricate protein protein interaction network underlying the assembly of the MC, the stoichiometry of the five TssNQOPR components., tTheir predicted structures were validated using crosslinking mass-spectrometry and we assessed the structural homology with known proteins. Importantly, we determine the connection between the T6SSiii MC and the otherwise conserved baseplate involving the hub protein Tss.Finally, phylogenomic analysis of the distribution of T6SSiii MC genes across the phylum Bacteroidota highlights patterns of conservation including the invariant

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Escherichia Coli

SUBMITTER: Florian Stengel

LAB HEAD: Florian Stengel

PROVIDER: PXD042118 | Pride | 2024-01-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F2207_orthj_016.mzXML	Mzxml
	F2207_orthj_016.raw	Raw
	F2207_orthj_017.mzXML	Mzxml
	F2207_orthj_017.raw	Raw
	F2207_orthj_019.mzXML	Mzxml

Items per page:

1 - 5 of 22

Similar Datasets

RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins

Project description:Pseudomonas aeruginosa uses three type six secretion systems (H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and compete with microbial competitors. These T6SS machines can be loaded with a variety of effectors/toxins, many being associated with a specific VgrG. How P. aeruginosa transcriptionally coordinates the three main T6SS clusters and the multiple vgrG islands spread through the genome is unknown. Here we show an unprecedented level of control of the regulator RsmA in repressing most known T6SS-related genes. Moreover, it is noticeable that a sigma factor activator (SFA) protein is encoded in each of H2- and H3-T6SS clusters, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins that usually work in concert with the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs of P. aeruginosa by activating the H2-T6SS but repressing the H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of all H2-T6SS-linked VgrG and effector arsenal to enable very effective interbacterial killing. Such RpoN-dependent control is exerted both directly and indirectly. The function of the SFA protein is specific since the H3-T6SS associated Sfa3 cannot complement loss of Sfa2. Our study further delineates the multiple regulatory mechanisms that modulate the deployment of an arsenal of T6SS effectors likely to respond and adapt to a range of environmental conditions that a versatile organism like P. aeruginosa would encounter.

2022-02-23 | GSE185398 | GEO

RNAseq of Mucor strains cultured on potato dextrose agar (PDA)

Project description:Mucor species belongs to the Mucorales order within the phylum Mucoromycota, an early diverging fungal lineage. The purpose of this study was to investigate at the transcriptome scale the similarities and differences that could be linked to different lifestyles. Five strains pertaining to five species were studied: M. fuscus and M. lanceolatus, two species used in cheese ripening, M. racemosus, a recurrent cheese spoiler sometimes described as an opportunistic pathogen, M. circinelloides, often described as an opportunistic pathogen and M. endophyticus, a plant endophyte species.

2018-09-01 | E-MTAB-6453 | biostudies-arrayexpress

Expression data from melanosis coli (MC)

2016-05-30 | GSE78933 | GEO

Expression data from melanosis coli (MC)

Project description:There is still a big debate about the correlation between melanosis coli (MC) and carcinoma. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human colonic mucosa with or without MC and try to investigate MC from gene aspect, eventually to demonstrate whether thereâs a certain correlation between MC and carcinoma. GeneChipÂ® Human Transcriptome Array 2.0 (HTA 2.0) microarrays were adopted. The expression profile of lncRNAs and mRNA were tested in five colon tissue biopsy specimen of MC patients and five demographically-matched controls. This study recruited a total of five MC patients and five coupled matched controls. All specimens were obtained from colonoscopy. The fresh specimens of colon tissues form MC patients and control patients were washed with RNAase free water and put into RNAlater (Qiagen) immediately and frozen in -80Â°C. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways.

2016-05-30 | E-GEOD-78933 | biostudies-arrayexpress

RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretion

Project description:We report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters.

2017-10-09 | GSE104716 | GEO

ClpV3 affects pathogenicity in Pseudomonas aeruginosa

Project description:ClpV3 is a cytoplasmic AAA+ ATPase protein and is an essential component of H3-T6SS in Pseudomonas aeruginosa. Here, we report that an H3-T6SS deletion mutant PAO1(ΔclpV3) significantly affected the virulence-related phenotypes including pyocyanin production, biofilm formation, proteolytic activity and motilities. Most interestingly, the expression of T3SS genes was markedly affected, indicating a strong link between H3-T6SS and T3SS. RNA-Sequencing was performed to globally identify the genes differentially expressed when H3-T6SS was inactivated and the results obtained could be well correlated to the observed phenotypes.

2020-04-20 | GSE148116 | GEO

Tempo-Seq targeted RNA sequencing of the HepaRG cell line treated with aflatoxin B1, benzo[a]pyrene, cyclosporin A, rotenone and thrichostatin A over a range of chemical concentrations and exposure time points

Project description:The experiment investigates the effects of five well-known chemicals on the transcriptome of the HepaRG cell line, a metabolically competent hepatic cell line. The cells were treated individually with an increasing concentrations of aflatoxin B1, benzo[a]pyrene, cyclosporine A, rotenone or trichostatin A at five exposure time points followed by targeted RNA-seq using TempO-Seq technology (the panel of human whole transcriptome). The aim of the study was to explore how and to what extent the point-of-departure (POD) obtained from an in vitro transcriptomics study varied as a function of exposure time.

2023-08-01 | E-MTAB-13168 | biostudies-arrayexpress

Role of adhesion receptors in mast cell disease-evolution

Project description:Systemic mastocytosis (SM) is an incurable neoplasm characterized by abnormal accumulation of neoplastic mast cells (MC) in vascularized organs. In indolent SM, MC express several different adhesion-molecules including CD2 and CD58, and form focal tissue-aggregates, whereas in advanced SM, MC often lack CD2 and produce a more diffuse infiltration-pattern. To explore the functional role of CD2 in the pathology of SM, stable CD2+ and CD2− subclones of the human MC-leukemia cell line HMC-1 were generated and injected intraperitoneally into pfp/rag2 mice. CD2+ HMC-1 cells formed solid mastocytomas in the peritoneum and lungs, whereas CD2− cells produced diffuse infiltration. CD2+ and CD2− HMC-1 subclones all displayed the driver-mutant KIT D816V, exhibited the same growth-kinetics, and displayed identical adhesion-receptors including CD44 and selectin-ligands. To explore the mechanism of organ invasion, E- and P-selectin-deficient scid mice (scid-select) were employed. While massive HMC-1 infiltrates were detected in the lungs of control mice, infiltration was markedly reduced or absent in scid-select mice. The invasion-receptor CD44 was detectable in all MC infiltrates, with most abundant expression in the invasion-front. Together, our data show that selectins mediate organ-invasion of MC and CD2-CD58 interactions contribute to a more focal infiltration-pattern which is lost during progression to MC leukemia. HMC1 cells were sorted by FACS for expression of CD2 surface expression. 2 subclones were obtained (CD2+ or CD2-) and compared by gene expression profiling using U133 plus 2.0 GeneChips

2013-01-01 | E-GEOD-33504 | biostudies-arrayexpress

Transcriptomic changes in Cinachyrella cf cavernosa as a response to spatial competition

Project description:Demosponge Cinachyrella cf cavernosa is an inter-tidal sponge. It is found in competition with soft coral Zoanthus sansibaricus and macroalgae Dictyota ciliatum. The effect of these two spatial competitors on the gene expression profile of the sponge is checked. Sponges are collected from three distinct situations, 1. sponge without competitors, 2. sponge in competition with algae, and 3. sponge in competition with soft coral. Each group has three biological replicates.

2023-04-25 | E-MTAB-9052 | biostudies-arrayexpress

The T6SSs of the entomopathogenic Photorhabdus laumondii revealed interbacterial competition and cross-link with diverse Photorhabdus-virulence mechanisms

Project description:Secretion systems are used as weapons by a variety of Gram-negative bacteria. Among them the Type VI Secretion System (T6SS) gained more interest throughout the last years. The system functions as a molecular nano-weapon: it is used in inter-kingdom competition by various bacteria to deliver toxic effectors in target cells. Here we describe the role of the T6SS in Photorhabdus laumondii subsp. laumondii strain DJC, an entomopathogenic biocontrol agent able to live in different environmental niches, such as in symbiosis with nematodes and in the rhizosphere on plant roots. Using bioinformatic and protein motif analyses we identified four T6SS gene clusters (T6SS-1, T6SS-2, T6SS-3 and T6SS-4) and multiple orphan T6SS related genes in the genome of P. laumondii. Furthermore, we highlighted 11 T6SS effector-immunity pairs, including three undescribed membrane disrupting effectors, each with putatively different antibacterial activities. By label-free mass spectrometry of P. laumondii wild type cells and respective T6SS-deficient strains, we could point out a cross-link between T6SS and other Photorhabdus’ virulence related mechanisms such as PVCs, T3SS and pyocins. Furthermore, a change in motility as well as in the secondary metabolism was observed upon T6SS-deficiency. Here, we shed light on the T6SS in P. laumondii DJC and suggesting a cross-link of various virulence mechanisms, which could help to gain knowledge on T6SS and better figure out the Photorhabdus ability to live in polymicrobial environments.

2024-04-05 | PXD035720 | Pride

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