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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

ABSTRACT: 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

PROVIDER: PRJNA976050 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24733149_1.fastq.gz	Fastqsanger.gz
	SRR24733149_2.fastq.gz	Fastqsanger.gz
	SRR24733150_1.fastq.gz	Fastqsanger.gz
	SRR24733150_2.fastq.gz	Fastqsanger.gz
	SRR24733151_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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

Effect of Smc and interaction with ParA on ParB binding to DNA in Pseudomonas aeruginosa

Project description:In the majority of bacterial species, the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target parS sequence(s), assists in the chromosome partitioning. ParB forms large nucleoprotein complexes at parS(s), located in the vicinity of oriC, which after replication are subsequently relocated by ParA to polar positions. It was shown that ParB-parS complexes are loading platforms for structural maintenance of chromosome (Smc) proteins, which juxtapose the two arms of the circular chromosome. In this work, we characterized the Pseudomonas aeruginosa ParB interactions with DNA in the absence of Smc and interaction with the cognate ParA using chromatin immunoprecipitation-sequencing (ChIPseq). We show that in strains lacking Smc or strains with disturbed ParB-ParA interactions (ParA L84K or ParB G11A mutations) ParB is able to bind and spread around parS1-4 cluster and still binds to half-parS sites. Comparison of the ratio between the number of ChIP-seq reads mapping to region around parS1-4 with those mapping to ChIPseq peaks containing half-parSs indicate no major effect of the twod factors on the extent of ParB spreading, thus suggesting that the mechanisms controlling ParB association with the DNA do not involve interaction with cognate ParA partner and Smc.

2022-12-17 | GSE213881 | GEO

A CTP-dependent gating mechanism enables ParB spreading on DNA

Project description:A CTP-dependent gating mechanism enables ParB spreading on DNA

| PRJNA714673 | ENA

Structural and biochemical analyses of Caulobacter crescentus ParB reveal the role of its N-terminal domain in chromosome segregation

Project description:The tripartite ParA-ParB-parS complex ensures faithful chromosome segregation in the majority of bacterial species. ParB nucleates on the centromere-like parS site and spreads to neighboring DNA to form a network of protein-DNA complexes. This nucleoprotein network in turn interacts with ParA to partition the parS locus, hence the chromosome to each daughter cell. Here, we determine the co-crystal structure of the C-terminal domain truncated ParB-parS complex from Caulobacter crescentus, and show that its N-terminal domain is inherently flexible and adopts multiple different conformations. We propose that the flexibility of the N-terminal domain might facilitate the spreading of ParB on the chromosome. Next, using ChIP-seq we show that ParBs from different bacterial species exhibit variation in their intrinsic capability for spreading, and that the N-terminal domain rather than the C-terminal domain is the main determinant for the variation in spreading. Finally, we show that the C-terminal domain of Caulobacter ParB does not possess non-specific DNA-binding activity in vitro. Engineered ParB variants with enhanced non-specific DNA-binding activity condense DNA in vitro but do not spread further than a wild-type protein in vivo. Taken together, our results emphasize the central role of the N-terminal domain in ParB spreading and faithful chromosome segregation.

2020-07-22 | GSE134665 | GEO

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

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

| PRJNA975514 | ENA

The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes

Project description:DNA partitioning CTPases of the ParB family mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centro-meric region of target DNA molecules and then spread laterally to form large nucleoprotein complexes that serve as docking points for the DNA segregation machinery. Here, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. Moreover, we solve crystal structures of ParB in the pre- and post-hydrolysis state and provide insight into the catalytic mechanism underlying nucleotide hydrolysis. The characterization of CTPase-deficient ParB variants reveals that CTP hydrolysis serves as a timing mechanism to control the sliding time of ParB. Hyperstable clamps are trapped on the DNA, leading to excessing spreading and severe chromosome segregation defects in vivo. These findings clarify the role of the ParB CTPase cycle in partition complex dynamics and function and thus complete our understanding of this prototypic CTP-dependent molecular switch.

2021-09-24 | GSE174037 | GEO

ChIPseq analysis of ParB binding to parSs and half-parSs in Pseudomonas aeruginosa under different environmental conditions and RNAseq analysis of selected half-parS removal on transcriptome

Project description:ChIPseq analysis of ParB binding to parSs and half-parSs in Pseudomonas aeruginosa under different environmental conditions and RNAseq analysis of selected half-parS removal on transcriptome

| PRJNA975961 | ENA

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

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