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Series GSE129285 Query DataSets for GSE129285
Status Public on Aug 05, 2019
Title Diversification of DNA-binding specificity via permissive and specificity-switching mutations in the ParB/Noc protein family
Organism Escherichia coli
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Specific interactions between proteins and DNA are essential to many biological processes. Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity, and that mutational paths to a new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc, and in a broader context, might be useful in understanding the evolution of other classes of DNA-binding proteins.
 
Overall design Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Escherichia coli (see the supplementary Materials and Methods for the exact treatment that were applied to each strain). Bacterial one-hybrid (B1H) with deep seqeuncing i.e. deep mutational scanning experiments were performed using plasmid DNA extracted from cells that were either selected on M9 minimal medium lacking (or supplemented) with histidine.
Web link https://doi.org/10.1016/j.celrep.2020.107928
 
Contributor(s) Le TB, Tran NT, Jalal AS, Stevenson SE, Tan X, Lawson DM, Lo R, Chan EW, Noy A
Citation(s) 32698006
Submission date Apr 03, 2019
Last update date Jul 23, 2020
Contact name Tung Ba Khanh Le
E-mail(s) tung.le@jic.ac.uk
Phone 01603450776
Organization name John Innes Centre
Department Department of Molecular Microbiology
Lab www.tunglelab.org
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (1)
GPL18133 Illumina HiSeq 2500 (Escherichia coli)
Samples (30)
GSM3703972 LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Agrobacterium_tumefaciens_ParB
GSM3703973 LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Bacillus_subtilis_Noc
GSM3703974 LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Bacillus_subtilis_ParB
Relations
BioProject PRJNA530746
SRA SRP190457

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129285_RAW.tar 268.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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