The early T4 protein, MotB, compacts host DNA and disrupts H-NS dependent repression.
Purpose: We investigated the effect of the T4 MotB protein on E. coli gene expression Method: BL21(DE3) E. coli containing either pNW129 or pNW129-MotB were grown to early log phase (OD600 ~ 0.3)  then induced with 0.2% arabinose for 20 minutes. Cells were then harvested and total RNA was isolated. The cDNA library was prepared using a modified RNATagSeq workflow as previously described (Shishkin, A.A. et al. 2015 Nat Methods). Optimum fragmentation of the total RNA samples in this library was determined to be 3 min at 94C in FastAP buffer (Thermo Fischer Scientific).  The cDNA Library was run on a Bioanalyzer using the Agilent High Sensitivity DNA Kit to evaluate the quality of the library.  The concentration of the cDNA library was determined by qPCR using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the single-end 50 bp Sequencing Kit (Illumina, San Diego, CA, USA). RNA-seq data was processed as previously described using E. coli B str. DE3 (NC_012971.2) as the reference genome.  Differential expression between conditions was represented as a fold change, and genes with both a fold change =2 and adjusted p value = 0.05 were considered significant. Results: RNA-seq data revealed that the expression of genes encoded in the cryptic prograge Lambda DE3 as well as an additional 29 of E. coli genes were significantly increased after motB expression. Conclusion: T4 MotB is a DNA binding protein that compacts host DNA and disrupts H-NS dependent repression. Overall design: To determine the effect of the T4 MotB protein on E. coli  gene expression, RNAseq was performed for BL21 (DE3) E. coli  producing T4 MotB for 20 minutes.