ChIP-seq of the R-tailocin locus-specific LexA-related regulator PrtR1, two H-NS-like proteins MvaT and MvaV and the cell cycle-associated protein ParB
ChIP-seq of the R-tailocin locus-specific LexA-related regulator PrtR1, two H-NS-like proteins MvaT and MvaV and the cell cycle-associated protein ParB
Pseudomonas protegens CHA0 is type strain widely used as an environmental model. ChIP was performed Pseudomonas protegens mutants with the proteins of interest (MvaT, MvaV, PrtR1 and ParB) flagged with a V5 in C-terminal. Cultures of the strains were restarted from overnights into fresh NYB at a ratio of 1:100. Once the cultures reached the exponential growth phase (OD600nm of 0.4-0.6), they were either induced with mitomycin C (9 nM) or were not induced for 3 h. Immunoprecipitations were done following a protocol from Antar et al. (DOI: 10.1126/sciadv.abj2854) and adapted for CHA0.  DNA was sheared using a Covaris S220 (settings: 50 ÂµL in microTUBES with AFA fiber; peak incident power, 175 W; duty factor, 10 %; cycles per burst, 200; treatment time, 120 s) and SPRI beads were used to purify the DNA at a 2.0 X ratio. NuGen Ovation Ultra Low system v2 (Tecan Trading AG) with 15 cycles of PCR amplification and using a unique dual indexing strategy was used to prepare the library.