title: Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function.
abstract: Histone-like protein H1 (H-NS) family proteins are nucleoid-associated proteins (NAPs) conserved among many bacterial species. The IncP-7 plasmid pCAR1 is transmissible among various Pseudomonas strains and carries a gene encoding the H-NS family protein, Pmr. Pseudomonas putida KT2440 is a host of pCAR1, which harbors five genes encoding the H-NS family proteins PP_1366 (TurA), PP_3765 (TurB), PP_0017 (TurC), PP_3693 (TurD), and PP_2947 (TurE). Quantitative reverse transcription-PCR (qRT-PCR) demonstrated that the presence of pCAR1 does not affect the transcription of these five genes and that only pmr, turA, and turB were primarily transcribed in KT2440(pCAR1). In vitro pull-down assays revealed that Pmr strongly interacted with itself and with TurA, TurB, and TurE. Transcriptome comparisons of the pmr disruptant, KT2440, and KT2440(pCAR1) strains indicated that pmr disruption had greater effects on the host transcriptome than did pCAR1 carriage. The transcriptional levels of some genes that increased with pCAR1 carriage, such as the mexEF-oprN efflux pump genes and parI, reverted with pmr disruption to levels in pCAR1-free KT2440. Transcriptional levels of putative horizontally acquired host genes were not altered by pCAR1 carriage but were altered by pmr disruption. Identification of genome-wide Pmr binding sites by ChAP-chip (chromatin affinity purification coupled with high-density tiling chip) analysis demonstrated that Pmr preferentially binds to horizontally acquired DNA regions. The Pmr binding sites overlapped well with the location of the genes differentially transcribed following pmr disruption on both the plasmid and the chromosome. Our findings indicate that Pmr is a key factor in optimizing gene transcription on pCAR1 and the host chromosome.
authors.affiliation: Biotechnology Research Center and Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Choong-Soo
authors.initials: CS
authors.lastname: Yun
authors.forename: Chiho
authors.initials: C
authors.lastname: Suzuki
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Naito
authors.forename: Toshiharu
authors.initials: T
authors.lastname: Takeda
authors.forename: Yurika
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Fumiya
authors.initials: F
authors.lastname: Sai
authors.forename: Tsuguno
authors.initials: T
authors.lastname: Terabayashi
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Miyakoshi
authors.forename: Masaki
authors.initials: M
authors.lastname: Shintani
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nishida
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Yamane
authors.forename: Hideaki
authors.initials: H
authors.lastname: Nojiri
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D015153:Blotting, Western; D004268:DNA-Binding Proteins / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D010957:Plasmids / Q000235:genetics*; D011485:Protein Binding; D016958:Pseudomonas putida / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria