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Bacillus subtilis: Smc-TAP ChIP-on-chip

ABSTRACT: Genome-wide analysis of Smc distribution using ChIP-on-chip ChIP DNA versus Input DNA Keywords: ChIP-chip Combined ChIP and Input DNA from three independent experiments on single array

ORGANISM(S): Bacillus subtilis

SUBMITTER: Stephan Gruber

PROVIDER: E-GEOD-14693 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis.

Gruber Stephan S Errington Jeff J

Cell 20090501 4

Proper segregation of DNA replication products is essential in all cells. In Bacillus subtilis, two protein complexes have been implicated in this process: the ParAB homologs, Soj and Spo0J, and the bacterial Smc/ScpAB complex, also called condensin. Here we demonstrate that Smc is highly enriched in the region around the origin of replication, specifically near parS sites to which Spo0J binds and at highly transcribed genes. Furthermore, we find that efficient recruitment of Smc to a large regi ...[more]

PMID: 19450516

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Bacillus subtilis: Smc-TAP ChIP-on-chip

Project description:Genome-wide analysis of Smc distribution using ChIP-on-chip ChIP DNA versus Input DNA Keywords: ChIP-chip

2009-05-14 | GSE14693 | GEO

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

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

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

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2021-05-28 | E-MTAB-9821 | biostudies-arrayexpress

A low Smc flux avoids collisions and facilitates chromosome organization in B. subtilis

Project description:SMC complexes are widely conserved ATP-powered loop extrusion motors indispensable for the faithful segregation of chromosomes during cell division. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength and the distribution of Smc loading sites, the residence time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is rather limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.

2021-07-30 | GSE163573 | GEO

Control of Smc Coiled Coil Architecture by the ATPase Heads Facilitates Targeting to Chromosomal ParB/parS and Release onto Flanking DNA

Project description:Smc/ScpAB promotes chromosome segregation in prokaryotes, presumably by compacting and resolving nascent sister chromosomes. The underlying mechanisms, however, are poorly understood. Here, we investigate the role of the Smc ATPase activity in the recruitment of Smc/ScpAB to the Bacillus subtilis chromosome. We demonstrate that targeting of Smc/ScpAB to ParB/parS loading sites is strictly dependent on engagement of Smc head domains and relies on an open organization of the Smc coiled coils. We find that dimerization of the Smc hinge domain stabilizes closed Smc rods and hinders head engagement as well as chromosomal targeting. Conversely, the ScpAB sub-complex promotes head engagement and Smc rod opening and thereby facilitates recruitment of Smc to parS sites. Upon ATP hydrolysis, Smc/ScpAB is released from loading sites and relocates within the chromosomeâpresumably through translocation along DNA double helices. Our findings define an intermediate state in the process of chromosome organization by Smc. ChIP-Seq experiments were performed on wild type and mutant cells of Bacillus subtilis 1A700.

2016-02-18 | E-GEOD-76949 | biostudies-arrayexpress

In vivo evidence for ATPase-dependent DNA translocation by the Bacillus subtilis SMC condensin complex

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2018-08-09 | GSE95137 | GEO

Chromosome remodelling by SMC/Condensin in B. subtilis is regulated by Soj/ParA during growth and sporulation

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2022-04-01 | GSE192868 | GEO

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

Project description:Structural maintenance of chromosomes (SMC) complexes play critical roles in chromosome dynamics in virtually all organisms but how they function remains poorly understood. In Bacillus subtilis, SMC condensin complexes are topologically loaded at centromeric sites adjacent to the replication origin. Here we provide evidence that these ring-shaped assemblies tether the left and right chromosome arms together while traveling from the origin to the terminus (>2 Mb) at rates >50kb/min. Condensin movement scales linearly with time arguing for an active transport mechanism. These data support a model in which SMC complexes function by processively enlarging DNA loops. Loop formation followed by processive enlargement provides a mechanism for how condensin complexes compact and resolve sister chromatids in mitosis and how cohesin generates topologically associating domains (TADs) during interphase.

2017-02-03 | GSE85612 | GEO

Bacillus subtilis

Project description:Bacillus subtilis: Smc-TAP ChIP-on-chip

| PRJNA112325 | ENA

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

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.

2022-06-23 | GSE206446 | GEO

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