 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 17, 2022 |
| Title |
Effect of Smc and interaction with ParA on ParB binding to DNA in Pseudomonas aeruginosa |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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.
|
| |
|
| Overall design |
Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1, was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis was performed on parental strain, Δsmc, parAstop Δsmc, and strains expressing ParB G11A or ParA L84K. A ΔparB strain was used as a background control. Cells were grown under in L broth until OD600 = 0.5. The immunoprecipitation was performed with polyclonal anti ParB antibodies, raised in rabbit and affinity purified (as in Reznekov et al., 1996, Genes Cells 1:529-542) and two replicates were performed for each strain (with the exception of ΔparB .
|
| |
|
| Contributor(s) |
Kawalek A, Bartosik AA, Gawor J, Zuchniewicz K, Gromadka R, Jagura-Burdzy G |
| Citation(s) |
36622167 |
| Submission date |
Sep 21, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Adam Kawałek |
| E-mail(s) |
a.kawalek@ibb.waw.pl
|
| Phone |
+48225921216
|
| Organization name |
Institute of Biochemistry and Biophysics, PAS
|
| Department |
Department of Microbial Biochemistry
|
| Street address |
Pawinskiego 5A
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platforms (1) |
| GPL21297 |
Illumina NextSeq 500 (Pseudomonas aeruginosa) |
|
| Samples (11)
|
|
| Relations |
| BioProject |
PRJNA882840 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213881_CP032126.bed.gz |
60.5 Kb |
(ftp)(http) |
BED |
| GSE213881_CP032126.fa.gz |
1.9 Mb |
(ftp)(http) |
FA |
| GSE213881_CP032126_PA_names.bed.gz |
61.4 Kb |
(ftp)(http) |
BED |
| GSE213881_RAW.tar |
286.1 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...