Abstract
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 KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), and KT2440(pCAR1Δpmr) 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, KT2440ΔturA, KT2440ΔturB) and four pCAR1-harboring strains [KT2440(pCAR1), KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), KT2440(pCAR1Δpmr)], 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 KT2440ΔturA and KT2440ΔturB did not overlap with those in KT2440ΔturA(pCAR1) and KT2440ΔturB(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.
Highlights
Bacteria have defense systems to protect themselves from foreign-derived, referred to as xenogeneic, DNA
From transcriptome analyses using Pseudomonas putida KT2440 as a host of pCAR1 and pCAR1 pmr, we previously found that Pmr has a “stealth” function resembling that of Sfh, while transcription levels of some genes on the chromosome and pCAR1 seemed to be regulated by Pmr (Yun et al, 2010)
The results revealed that differentially transcribed genes after the deletion of turA, turB, or pmr compared with the wild-type KT2440(pCAR1) were not so overlapped each other, especially when pmr was deleted
Summary
Bacteria have defense systems to protect themselves from foreign-derived, referred to as xenogeneic, DNA. H-NS family proteins, a major family of bacterial nucleoid-associated proteins, are well-known xenogeneic silencers which affect both nucleoid compaction and global gene regulation (Dorman, 2009; Ali et al, 2012; Singh et al, 2016) They preferably bind to AT-rich regions, which are usually acquired by horizontal gene transfer, and repress transcription from those regions (Grainger et al, 2006; Lucchini et al, 2006; Navarre et al, 2006; Oshima et al, 2006). Among the five genes encoding MvaT homologs in KT2440, turA and turB are considered to be transcribed predominantly, and their protein expression level was previously determined (Yuste et al, 2006; Renzi et al, 2010; Yun et al, 2010; Sun et al, 2017). Nelson et al (2002) This study This study Shintani et al (2006); Miyakoshi et al (2007) Yun et al (2016) Yun et al (2016) Suzuki-Minakuchi et al (2015)
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