Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

1 Citations

0 Reanalyses

0 Downloads

Omics score: 0

S.lividans TK24 sigma-factor deletions

ABSTRACT: Characterization of S.lividans TK24 secreted proteome changes upon deletion of certain sigma factors.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Streptomyces Lividans Tk24

SUBMITTER: Konstantinos Tsolis

LAB HEAD: Tassos Economou

PROVIDER: PXD006818 | Pride | 2019-02-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Secretome Dynamics in a Gram-Positive Bacterial Model.

Tsolis Konstantinos C KC Hamed Mohamed Belal MB Simoens Kenneth K Koepff Joachim J Busche Tobias T Rückert Christian C Oldiges Marco M Kalinowski Jörn J Anné Jozef J Kormanec Jan J Bernaerts Kristel K Karamanou Spyridoula S Economou Anastassios A

Molecular & cellular proteomics : MCP 20181129 3

Protein secretion is a central biological process in all organisms. Most studies dissecting bacterial secretion mechanisms have focused on Gram-negative cell envelopes such as that of <i>Escherichia coli</i> However, proteomics analyses in Gram negatives is hampered by their outer membrane. Here we studied protein secretion in the Gram-positive bacterium <i>Streptomyces lividans</i> TK24, in which most of the secretome is released in the growth medium. We monitored changes of the secretome as a ...[more]

PMID: 30498012

Similar Datasets

S.lividans TK24 protease deletions

Project description:Characterization of S.lividans TK24 secreted proteome changes upon deletion of certain proteases.

2018-06-28 | PXD006819 | Pride

Identification by ChIP-Seq of the binding sites of the sigma factor WhiG in the genome of Streptomyces venezuelae

Project description:The WhiG sigma factor gene is required for spore formation is Streptomyces venezuelae. It is similar to the FliA sigma factor of E. coli. WhiG deletion strains are able to make aerial hyphae but are defective in the spore maturation. This ChIP-Seq experiment was carried out to determine all the binding sites WhiG binds to in the genome of Streptomyces venezuelae. Anti-WhiG polyclonal antibodies were used for ChIP-Seq of the wild type (WT) strain after 34 hours of growth in shaken cultures. A WhiG deletion strain was made and anti-WhiG antibodies were used for ChIP-Seq in the deletion strain after 34 hours of growth in shaken cultures. This was used as the negative control and ChIP-Seq peak positions in this were disregarded in the WT.

2019-08-01 | E-MTAB-8160 | biostudies-arrayexpress

SigX ECF sigma factor deletion mutant expression profile in Pseudomonas aeruginosa in M9 minimal medium (M9G)

Project description:Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in minimal medium with glucose as carbon source (M9G). SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF in Pseudomonas aeruginosa. Deletion of the ECF sigma factor sigX gene provide insights into the SigX role in several virulence and biofilm- related phenotypes in Pseudomonas aeruginosa.

2014-01-01 | GSE51076 | GEO

Identification by ChIP-Seq of the binding sites of the extracytoplasmic function (ECF) sigma factor SigE in the genome of Streptomyces coelicolor A3(2) M600.

Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30 minutes. A 3xFLAG tagged SigE was introduced in a SigE deletion strain and ChIP-Seq was carried out using M2 (Sigma Aldrich A2220) gel suspension. Non-immunoprecipitated (total) DNA preparations were used for background determination and the wild type M600 was used as the negative control.

2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress

Analysis of sigma factor-dependent gene expression in Pseudomonas aeruginosa by RNA sequencing

Project description:Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including sigma factor-dependent mRNA profiling was performed to define the primary regulon of each sigma factor. Sigma factor hyper-expressing strains harboring the sigma factor gene in trans under control of the araBAD promoter and sigma factor deletion mutants were constructed. Under optimal conditions regarding sigma factor activity and optional induction of sigma factor expression, bacteria were harvested and total RNA was extracted. Upon mRNA enrichment, RNA was fragmented and ligated to specific RNA-adapters containing a hexameric barcode sequence for multiplexing. These RNA-libraries were reverse transcribed and amplified resulting in cDNA libraries which were sequenced on Illumina platforms. Sequence reads were separated according to their barcodes and barcode sequences were removed. The short reads were mapped to the genome sequence of the reference strain P. aeruginosa PA14 wild-type using stampy with default settings. The R package DESeq was used for differential gene expression analysis.

2015-02-12 | E-GEOD-54998 | biostudies-arrayexpress

A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa

Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor.

2009-04-21 | GSE15697 | GEO

Analysis of sigma factor-dependent gene expression in Pseudomonas aeruginosa by RNA sequencing

2015-02-12 | GSE54998 | GEO

Predictive design of sigma factor-specific promoters

Project description:Predictive design of sigma factor-specific promoters

| PRJEB36433 | ENA

Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity

Project description:We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. In accordance, a sigX deletion mutant exhibited an altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative σ factor SigX revealing its role in complex virulence-associated phenotypes in P. aeruginosa.

2013-11-11 | GSE50937 | GEO

Sigma virus

Project description:sigma virus DMelSV raw sequence reads

| PRJNA326864 | ENA