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H-NS family proteins regulate the expression of many genes by preferably binding to AT-rich genomic regions and altering DNA topology. They are found in both bacterial chromosomes and plasmids, and plasmid-encoded H-NS family proteins have sometimes been suggested to act as a molecular backup of the chromosomally encoded ones. Pmr is an H-NS family protein encoded on the catabolic plasmid pCAR1, which belongs to incompatibility P-7 group. We have investigated the function of Pmr in  Pseudomonas putida  KT2440, where two H-NS family proteins (TurA and TurB) encoded on the chromosome are expressed predominantly. Previous transcriptome analyses suggested that TurA, TurB, and Pmr cooperatively regulate numerous genes, but the differentially transcribed genes in KT2440Δ turA (pCAR1), KT2440Δ turB (pCAR1), and KT2440(pCAR1Δ pmr ) compared with those in KT2440(pCAR1) were somewhat different. Here, we performed RNA sequencing analyses to compare the differentially transcribed genes after the deletion of  turA  or  turB  in KT2440, and  turA ,  turB  or  pmr  in KT2440(pCAR1). Three pCAR1-free strains (KT2440, KT2440Δ turA , KT2440Δ turB ) and four pCAR1-harboring strains [KT2440(pCAR1), KT2440Δ turA (pCAR1), KT2440Δ turB (pCAR1), KT2440(pCAR1Δ pmr )], grown until the log and stationary phases, were used. In KT2440, TurA was the major H-NS family protein regulating a large number and wide range of genes, and both TurA and TurB were suggested to functionally compensate each other, particularly during the stationary phase. In KT2440(pCAR1), the numbers of differentially transcribed genes after the deletion of  turA  or  turB  drastically increased compared to those in KT2440. Notably, more than half of the differentially transcribed genes in KT2440Δ turA  and KT2440Δ turB  did not overlap with those in KT2440Δ turA (pCAR1) and KT2440Δ turB (pCAR1). This dynamic change could be explained by the acquisition of pCAR1 itself and the expression of Pmr. After pCAR1 was transferred into the host, TurA and TurB could be detached from the chromosome of KT2440 and they could newly bind to pCAR1. Moreover, Pmr could reconstitute the chromosome-binding heteromeric oligomers which were formed by TurA and TurB. Our study revealed that horizontal transfer of a plasmid changes the transcriptional network of the chromosomally encoded H-NS family proteins.

H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1