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ParBF DNA binding profiles from variants of the CTP binding motif

ABSTRACT: ParBF DNA binding profiles from variants of the CTP binding motif

PROVIDER: PRJNA1221528 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR32282009.fastq.gz	Fastqsanger.gz
	SRR32282011.fastq.gz	Fastqsanger.gz
	SRR32282013.fastq.gz	Fastqsanger.gz
	SRR32282014.fastq.gz	Fastqsanger.gz

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ParBF DNA binding profiles from variants of the CTP binding motif

Project description:We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli, investigates the impact of mutations in the CTP binding motif BoxIII on ParBF DNA binding profiles in vivo. We found that ParBF-N153A allele binds to parS as WT but is impaired in clamp formation thus abolishing the long distance DNA binding on parS-proximal DNA. By contrast, ParBF-R156A DNA binding profile reveals that it binds to parS, converts to clamps that diffuse over several Kb and unbinds non-specific DNA in a similar way as WT. However, the reduction in ParB binding at proximity of parS revealed that ParBF-R156A is impaired in ParB-ParB interaction, thus preventing the assembly of ParB condensates.

2025-06-01 | GSE289093 | GEO

Binding and regulation of transcription by yeast Ste12 variants to drive mating and invasion phenotypes

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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.

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Project description:The ATP- and CTP-dependent ParA-ParB-parS segrosome is a macromolecular complex that segregates chromosomes/plasmids in most bacterial species. CTP binding and hydrolysis enable ParB to slide along DNA and to bridge and condense DNA, thereby dictating the size and dynamics of the tripartite ParABS complex. Several other evolutionarily distinct systems can also segregate DNA, although the full diversity of bacterial DNA partition systems remains unknown. Here, we identify a CTP-independent ParABS system that maintains the conjugative plasmid SCP2 in the filamentous bacterium Streptomyces coelicolor. We demonstrate that an SCP2 ParB-like protein, ParT, loads onto DNA at an 18-bp parS site and diffuses away to the adjacent DNA despite lacking an apparent CTPase domain and detectable NTPase activity. We further show that parS DNA facilitates ParT transition from loading to a diffusing state, allowing ParT to accumulate on DNA, and that ParT activates the ATPase activity of its cognate partner protein, ParA. Additionally, we identify numerous structural homologs of ParT, suggesting that CTP-independent diffusion on DNA might be more common than previously recognized. Overall, our findings reveal a CTP-independent DNA translocation as an alternative and unexpected mechanism for assembling a bacterial DNA segregation complex and suggest that CTP binding and hydrolysis are not universal features of ParABS-like systems.

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GABPα and CREB1 binding to double nucleotide polymorphisms of their consensus motifs and cooperative binding to the ETS-CRE motif (ACCGGAAGTGACGTCA).

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