Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis

To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). Compared with pf0-1, the most significantly downregulated genes were dndBCDE themselves due to the in-frame deletion in TT-5. Of the 6 up-regulated genes, two are phage-related proteins (Pfl01_1169 and Pfl01_3496); the rest are genes encoding a putative membrane protein (Pfl01_0900), xanthine dehydrogenase (Pfl01_1797), N-acetylmuramoyl-L-alanine amidase (Pfl01_5657) and a hypothetical protein (Pfl01_2488). The transcription levels of the differentially expressed genes varied to different degrees and the genes belong to different COG groups. Examination of global transcriptional variation in wild type P. fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant