Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq of the R-tailocin locus-specific LexA-related regulator PrtR1, two H-NS-like proteins MvaT and MvaV and the cell cycle-associated protein ParB

ABSTRACT: A ChIP-seq was used to identify the binding regions of the R-tailocin locus-specific LexA-related regulator PrtR1, two H-NS-like proteins MvaT and MvaV and the cell cycle-associated protein ParB in a R-tailocin inducing condition (with mitomycin C) and a non-inducing condition. We used Pseudomonas protegens CHA0 mutants that produce the protein of interest with a C-terminal V5-tag (MvaT-V5, MvaV-V5, PrtR-V5 and ParB-V5). We used CHA0 wild type without tagged proteins as a negative control.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Pseudomonas protegens

SUBMITTER: Clara Heiman

PROVIDER: E-MTAB-14721 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of wild type Pseudomonas protegens CHA0 and H-NS-like mutants ΔmvaT, ΔmvaV and ΔmvaTΔmvaV

Project description:A RNA-seq was used to test the effect of two DNA-damaging agents (mitomycin C and hydrogen peroxide) on gene expression in wild type Pseudomonas protegens CHA0 and three H-NS-like mutants: ΔmvaT, ΔmvaV and ΔmvaTΔmvaV.

2025-04-02 | E-MTAB-14715 | biostudies-arrayexpress

The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface

Project description:Chromosomes readily unlink from one another and segregate to daughter cells during cell division highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes mediate chromosome folding by DNA loop extrusion. In most bacteria, SMC complexes start loop extrusion at the ParB/parS partition complex formed near the replication origin. Whether they are recruited by recognizing a specific DNA structure in the partition complex or a protein component is unknown. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate chromosomes when transplanted into another organism. Using chimeric proteins and chemical cross-linking, we find that ParB binds to the Smc subunit directly. We map a binding interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex to initiate DNA loop extrusion.

2022-03-01 | GSE190491 | GEO

Genome-wide identification of ParB binding sites in Pseudomonas aeruginosa

Project description:ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in proper folding and initial separation of ori domains by binding to specific parS sites (palindromic centromere-like sequences), mainly localized close to oriC. Bioinformatic analyses identified 10 parS sequences in the Pseudomonas aeruginosa PAO1 genome. One parS from the parS1-parS4 cluster is required for ParB mediated chromosome segregation. To verify the binding of ParB to all known parSs in vivo as well as to identify additional ParB binding sites we performed chromation immunoprecipitation (ChIP) using polyclonal anti-ParB antibodies followed by high throughput sequencing. ChIP was performed with P. aeruginosa PAO1161 (WT) cells, PAO1161 pKB9 (ParB+++) cells with a slight, non-toxic ParB overproduction as well as with 3 strains containing parS modifications impairing ParB binding to these sites. The data confirmed ParB binding to all known parS sequences with the exception of parS5. Moreover, we identified more than a 1000 of new ParB-bound regions, majority of which contained a DNA motif corresponding to inner 7 nt from one arm of the parS palindrome. ParB interactions with these numerous sites could affect chromosome topology, compaction and gene expression classifying P. aeruginosa ParB as a Nucleoid Associated Protein (NAP).

2018-03-27 | GSE110158 | GEO

The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface [ChIP-seq]

2022-06-23 | GSE206446 | GEO

Impact of culture conditions on ParB distribution in Pseudomonas aeruginosa and analysis of ParB distribution in spreading deficient strains as well as half-parS25 strain

Project description:Chromosome segregation in Pseudomonas aeruginosa is assisted by the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target parS sequence(s). ParB forms a nucleoprotein complex around four parSs (parS1-parS4), which is positioned within the cell by ParA. Remarkably, ParB of P. aeruginosa binds to multiple heptanucleotides (half-parSs) scattered in the genome. In this work we analysed the influence of culturing conditions on ParB binding to DNA. Using chromatin immunoprecipitation-sequencing (ChIP-seq), we analysed patterns of genome occupancy by ParB in cells, with either coupling or uncoupling between replication and cell division. Our data indicated no altered preference of ParB to bind to individual half-parS sites under varying growth conditions, however a shift from parSs to half-parSs was evident in response to extended cell division time. The ChIP-seq analysis of strains expressing ParB variants unable to dislocate from parSs showed that ParB spreading ability is not required for ParB binding to half-parSs. Finally, a P. aeruginosa strain with mutated 27 half-parSs forming the strongest ParB ChIP-seq peaks was constructed and analysed showing changes in the ParB coverage of oriC region. Overall this work suggests the role of half-parSs in retaining ParB on the nucleoid within P. aeruginosa cells.

2023-08-03 | GSE233378 | GEO

Identification of ParB binding sites in vivo in Pseudomonas aeruginosa

Project description:To identify ParB binding sites in vivo, we performed ChIP experiments followed by high throughput sequencing using a 3xflag tagged version of ParB, in different genetic backgrounds. This allowed us to show that ParB binds in vivo mostly to 4 parS sites, located within 15 kb of oriC. We also identify 9 secondary ParB binding sites.

2016-10-18 | GSE87409 | GEO

Microarray analysis of the impact of ParB excess on gene expression in Pseudomonas aeruginosa

Project description:In Pseudomonas aeruginosa, partitioning protein ParB facilitates segregation of newly replicated chromosomes but is not essential for cell survival. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism. To identify primary targets of ParB, we analysed the impact of a slight increase in ParB amount on the transcriptome using microarrays. A several-fold increased ParB level does not cause recognizable phenotypic changes but leads to significant changes in the expression of 211 loci, including transcriptional regulators of operons involved in SOS response, virulence and adaptation. Most notably, the mRNA level of genes adjacent to high affinity ParB binding sites parS1-4 close to oriC is reduced. Our data support the role of partitioning protein ParB as a transcriptional regulator in Pseudomonas aeruginosa.

2017-07-25 | GSE95647 | GEO

ChIP-seq experiment of SMC-FLAG binding to Streptomyces venezuelae chromosome in wild type and parB knockout strain

Project description:We studied the binding of SMC protein to Streptomyces venezuelae chromosome during development of aerial hyphae (14 hour of growth) using SMC-FLAG protein. Additionally investigated the role of ParB protein in SMC DNA binding using parB deletion strain.

2021-05-28 | E-MTAB-9822 | biostudies-arrayexpress

A CTP-dependent gating mechanism enables ParB spreading on DNA

Project description:Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS to spread by sliding to the neighboring DNA. Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products may re-open the gates. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation and spreading.

2021-05-01 | GSE168968 | GEO

Transcriptome analysis of Pseudomonas aeruginosa strain, with 25 mutated half-parSs (ParB binding sites)

2023-08-03 | GSE233235 | GEO