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| Status |
Public on May 25, 2010 |
| 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 |
| Platform organisms |
Pseudomonas; Pseudomonas putida KT2440 |
| Sample organism |
Pseudomonas putida |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Expression profiling by genome tiling array
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| Summary |
H-NS family proteins are known as a member of nucleoid associated proteins (NAPs) conserved in genus Pseudomonas bacteria. Incompatibility group (Inc) P-7 archetype plasmid pCAR1 is transmissible among various Pseudomonas strains and carries genes encoding H-NS family protein, Pmr. P. putida KT2440 is one of pCAR1 hosts, which possesses five genes encoding H-NS family proteins, PP_1366 (TurA), PP_3765 (TurB), PP_0017 (TurC), PP_3693 (TurD), and PP_2947 (TurE) on its chromosome. Quantitative RT-PCR showed that the presence of Pmr did not affect on the transcriptions of genes encoding H-NS family proteins, and only Pmr, TurA and TurB were majorly transcribed. In vitro Pull down assay revealed that Pmr strongly interacted with Pmr itself and TurA, TurB, and TurE. Transcriptome comparisons of pmr disruptant, with KT2440 and KT2440(pCAR1) showed that the pmr disruption had larger effects on the host transcriptome than those by pCAR1 carriage. The transcriptional levels of some genes increased by pCAR1 carriage were reverted to those of pCAR1-free KT2440 by disruption of pmr, such as mexEFoprN genes for efflux pump, and parI. Transcriptional levels of many genes on the putative foreign DNA regions were not altered by carriage of pCAR1 but by pmr disruption. Identification of genome-wide Pmr binding sites by ChAP-chip analysis showed that Pmr preferentially binds to the foreign DNA region. Pmr binding sites were well overlapping with the location of the differentially transcribed genes by disruption of pmr. Our findings indicate that Pmr is a key factor to optimize the gene transcription onpCAR1 and host chromosome.
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| Overall design |
ChIP-chip: Pseudomonas putida KT2440 harboring pCAR1 cells ChIPed with His-tag ( C-terminus of pmr) vs Input in Pseudomonas putida KT2440 harboring pCAR1 cells
RNA mapping: 4 samples were compared including two biological replicates.
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| Contributor(s) |
Yun C, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F, Terabayashi T, Miyakoshi M, Shintani M, Nishida H, Yamane H, Nojiri H |
| Citation(s) |
20639326 |
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| Submission date |
May 24, 2010 |
| Last update date |
Dec 10, 2013 |
| Contact name |
Hideaki NOJIRI |
| E-mail(s) |
anojiri@mail.ecc.u-tokyo.ac.jp
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| Phone |
+81-3-5841-3064
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| Fax |
+81-3-5841-8030
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| URL |
http://park.itc.u-tokyo.ac.jp/biotec-res-ctr/kampo/eng/index.html
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| Organization name |
The University of Tokyo
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| Department |
Biotechnology Research Center
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| Lab |
Laboratory of Environmental Biochemistry
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| Street address |
1-1-1 Yayoi, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-8657 |
| Country |
Japan |
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| Platforms (2) |
| GPL6591 |
[pCAR1_8b520435F] Affymetrix CustomExpress IncP-7 plasmid pCAR1 Tiling Array |
| GPL8296 |
[KT2440b520511F] Pseudomonas putida KT2440 chromosome Array |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA126783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21968_RAW.tar |
113.4 Mb |
(http)(custom) |
TAR (of BAR, BED, CEL) |
| Processed data provided as supplementary file |
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