GEO DataSets

(Submitter supplied) Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB’s DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. more...

Organism:

Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28115 GPL23088

8 Samples

Download data: CSV

(Submitter supplied) To investigate the possible genes regulated by the DNA binding protein MraZ The bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5’ end of the dcw cluster and previous studies have described MraZ as a sequence-specific DNA binding protein. more...

Organism:

Bacillus subtilis PY79

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32384

4 Samples

Download data: TSV

(Submitter supplied) Many pathogens and symbionts contain multipartite genomes, but how they are stably maintained is poorly understood. The plant pathogen, Agrobacterium tumefaciens, contains four replicons. Recent work indicates that their replication origins cluster at cell poles in a manner that depends on their ParB-family centromeric proteins. Here, we provide evidence that centromeric clustering is mediated by interactions between these centromeric proteins. more...

Organism:

Agrobacterium tumefaciens; Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL28115 GPL30555

29 Samples

Download data: CSV, TXT, ZIP

(Submitter supplied) Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. more...

Organism:

Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL20691 GPL28115

81 Samples

Download data: CSV, TXT

(Submitter supplied) Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. more...

Organism:

Bacillus subtilis PY79

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23088

8 Samples

Download data: CSV

(Submitter supplied) Bacillus subtilis SMC complexes are topologically loaded at centromeric sites adjacent to the replication origin by the partitioning protein ParB. These ring-shaped ATPases then translocate down the left and right chromosome arms while tethering them together. Here we show that the site-specific recombinase XerD that resolves chromosome dimers is required to unload SMC tethers when they reach the terminus. more...

Organism:

Staphylococcus aureus; Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

5 related Platforms

104 Samples

Download data: CSV, TXT

(Submitter supplied) To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop extrusion process is largely unexplored, but recent experiments show that sites of high transcription may directionally affect condensin loop extrusion. more...

Organism:

Bacillus subtilis PY79

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23088 GPL20691

10 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacillus subtilis PY79; Bacillus subtilis

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL26622 GPL26620

5 Samples

Download data: CSV

(Submitter supplied) We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

Organism:

Bacillus subtilis PY79

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26620

4 Samples

Download data: CSV

(Submitter supplied) Structural maintenance of chromosomes (SMC) complexes shape the genomes of virtually all organisms but how they function remains incompletely understood. Recent studies in bacteria and eukaryotes have led to a unifying model in which these ring-shaped ATPases act along contiguous DNA segments processively enlarging DNA loops. In support of this model, single-molecule imaging experiments indicate that Saccharomyces cerevisiae condensin complexes can extrude DNA loops in an ATP hydrolysis dependent manner in vitro. more...

Organism:

Bacillus subtilis PY79

Type:

Other

Platform:

GPL23088

24 Samples

Download data: TXT

(Submitter supplied) The objective of the experiments was to identify non-essential genes required for mitigating the response DNA damage

Organism:

Bacillus subtilis PY79

Type:

Other

Platform:

GPL20121

57 Samples

Download data: CSV, FA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacillus subtilis PY79; Staphylococcus aureus subsp. aureus NCTC 8325

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20691 GPL23706 GPL22897

37 Samples

Download data: CSV

(Submitter supplied) Successive division events in the spherically shaped bacterium Staphylococcus aureus are oriented in three alternating perpendicular planes. The mechanisms that underlie this relatively unique pattern of division and coordinate it with chromosome segregation remain largely unknown. Thus far, the only known spatial regulator of division in this organism is the nucleoid occlusion protein Noc that inhibits assembly of the cytokinetic ring over the chromosome. more...

Organism:

Staphylococcus aureus subsp. aureus NCTC 8325; Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22897 GPL20691

20 Samples

Download data: CSV

(Submitter supplied) 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. more...

Organism:

Bacillus subtilis PY79

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20121 GPL20691

59 Samples

Download data: CSV, TXT

(Submitter supplied) SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms yet how they accomplish this remains elusive. In Bacillus subtilis, condensin is loaded at centromeric parS sites, where it encircles DNA and individualizes newly replicated origins. Using chromosome conformation capture and cytological assays, we show that condensin recruitment to origin-proximal parS sites is required for the juxtaposition of the two chromosome arms. more...

Organism:

Bacillus subtilis PY79

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20121 GPL20691

41 Samples

Download data: CSV, TXT