Shifts in the epigenomic landscapes of co-existing DNA phosphorothioates and methylation in Pseudomonas
PT modification is widely distributed in the bacterial genome, in which a sulfur atom replaces a non-bridging oxygen atom in DNA backbone. Its function is related to restriction modification, oxidative stress, and regulation of gene expression. By heterologously expressing the GpsATC modification system and the Gm6ATC modification system in E. coli HST04 strain, previous studies found that the PT modification and another restriction modification, the methylation modification, can share the same motif. However, bacteria in which both modifications naturally coexist in the same motif do not exist in nature. We found a bacterial strain S1 that naturally contains the GpsATC modification and used this strain to construct multiple modification systems to study the interactions between the multiple modifications. Our results showed that when the dam gene (G6mATC) is introduced, the two modifications can coexist in the same motif (Gps6mATC) and produce the new modification types (GpsATC); when another PT modification system (GPS GCC) is introduced, the two types of PT modification motifs (GpsGCC, GpsATC) coexist, with GpsGCC dominating. It also led to the emergence of the novel modification type CpsTGG/CpsCAG. All three models of multisystem coexistence resulted in shifts in modification sites and differences in gene expression. This study sheds light on the understanding of modification interactions and epigenetic networks. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas qingdaonensis strain S-1 and mutants