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Transcriptional network between pCAR1 and KT2440 chromosome

ABSTRACT: The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440. To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source. Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome. Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions. Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas. To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions. Keywords: Comparative transcriptome analysis

ORGANISM(S): Pseudomonas putida

PROVIDER: GSE7650 | GEO | 2007/05/01

SECONDARY ACCESSION(S): PRJNA99771

REPOSITORIES: GEO

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High-resolution mapping of the pCAR1 plasmid transcriptomes in Pseudomonas

Project description:High-resolution mapping of the pCAR1 plasmid transcriptomes in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) While plasmids are replicated autonomously in their hosts, the transcription of plasmid genes can be switched through horizontal transfer by the change in the transcriptional networks. To examine whether and how the plasmid genome is differentially expressed, we analyzed the transcriptomes of the 199,035-bp IncP-7 carbazole catabolic and conjugative plasmid pCAR1 in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) during growth on carbazole or succinate using the high-resolution tiling array. The tiling array successfully detected the relatively large catabolic operons, for which transcription was induced during growth on carbazole regardless of the host. Compared between the hosts, nearly identical regions of pCAR1 were transcribed, but two hypothetical operons, i.e., ORF100-108 and ORF145-146, were transcribed at higher levels in KT2440(pCAR1) than in CA10. We verified the differential expression in heterologous hosts using quantitative RT-PCR. The tiling array analysis clearly revealed the transcription start sites, for which the positions and extents agreed with the primer extension experiments. Our data demonstrate that the transcriptome of the transmissible plasmid is altered through horizontal transfer, and we identified probable genes that are involved in plasmid functions in various hosts. This approach can be used to visualize flexible prokaryotic transcriptomes comprehensively. Keywords: high-resolution RNA mapping

2008-10-18 | GSE10862 | GEO

Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1.

Project description:Plasmid carriage requires appropriate expression of the genes on the plasmid or host chromosome through cooperative transcriptional regulation. To clarify the impact of plasmid carriage on the host chromosome, we compared the chromosomal RNA maps of plasmid-free and plasmid-containing host strains using the incompatibility group P-7 archetype plasmid pCAR1, which is involved in carbazole degradation, and three distinct Pseudomonas strains. The possession of pCAR1 altered gene expression related to the iron acquisition systems in each host. Expression of the major siderophore pyoverdine was greater in plasmid-containing P. putida KT2440 and P. aeruginosa PAO1 than in the plasmid-free host strains, in part due to the expression of carbazole-degradative genes on pCAR1. The mexEFoprN operon encoding an efflux pump of the resistance-nodulation-cell division (RND) family was specifically upregulated by the carriage of pCAR1 in P. putida KT2440, whereas the expression of orthologous genes in the other species remained unaltered. Induction of the mexEFoprN genes increased the resistance of pCAR1-containing KT2440 to chloramphenicol compared to pCAR1-free KT2440. Our findings indicate that the possession of pCAR1 altered the growth rate of the host via the expression of genes on pCAR1 and the host chromosomes.

2009-12-25 | GSE15217 | GEO

Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in three Pseudomonas strains.

Project description:To elucidate the impact of the carriage of carbazole-degradative plasmid pCAR1 on biofilm formation by host bacteria, we compared biofilm morphology of pCAR1-free and pCAR1-carrying three Pseudomonas hosts: P. putida KT2440, P. aeruginosa PAO1 and P. fluorescens Pf0-1 using confocal laser scanning microscopy. Although pCAR1 carriage had no significant influence on biofilm formed by PAO1 and Pf0-1, pCAR1-carrying KT2440 became filamentous and formed flat biofilm, whereas pCAR1-free KT2440 formed mushroom-like biofilm. pCAR1 carries three genes encoding nucleoid-associated proteins (NAPs); Pmr, Pnd, and Phu. Because intensive filamentous morphology was observed in two double mutants (DpmrDpnd and DpmrDphu), these NAPs cooperatively suppress cell filamentation and flat biofilm formation in KT2440(pCAR1) cells. Based on the results of transcriptome analyses of these double mutants, we could find 32 candidate genes which may be involved in the filamentation of KT2440(pCAR1). Overproduction in KT2440 and KT2440(pCAR1) of three of candidate genes (PP_2193, PP_0308, or PP_0309) induced temporal filamentation of the cells, suggesting that pCAR1 induced the abnormal filamentous morphology of KT2440 cells by overexpression of plural genes including PP_2193, PP_0308, and PP_0309. In addition, pCAR1-borne NAPs suppress the morphological changes probably by decreasing the transcriptome change by pCAR1 carriage. The pCAR1 carriage impact of chromosomal RNA maps in biofilm formation.

2014-05-08 | E-GEOD-56856 | biostudies-arrayexpress

MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently (pCAR1)

Project description:MvaT proteins are recognized as a member of H-NS family proteins in pseudomonads. IncP-7 conjugative plasmid pCAR1, which was originally found in Pseudomonas resinovorans, carries an mvaT homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, it was previously reported that pmr and chromosomally-encoded homologous genes, turA and turB, are majorly transcribed, and that Pmr interacts with TurA and TurB in vitro (Yun et al. J. Bacteriol. 192:4720-4731, 2010). In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Modified ChIP-chip analyses suggested that the binding sites of Pmr, TurA, and TurB in P. putida KT2440(pCAR1) genome were almost identical; nevertheless, transcriptome analyses using deletion mutants of each MvaT protein gene at the log and early-stationary growth phases clearly suggested that their regulons were different with one another. Especially, significant dissimilarity of regulons was found between Pmr and other two proteins. Transcriptions of the larger number of genes were affected by Pmr deletion at the early-stationary phase than at the log phase, suggesting that Pmr minimizes the pCAR1 effects on host fitness more effectively at the early-stationary phase. On the other hand, similarity found between the regulons of TurA and TurB implied that they may have complementary roles as global transcriptional regulators in response to the plasmid carriage. ChIP-chip: Pseudomonas putida KT2440 harboring plasmid pCAR1 cells were ChIPed with His-tag (C-terminus of each MvaT homologs) and compared with input control. Transcriptome analysis: pCAR1 RNA maps of mvaT deletion mutants were compared with those of wild-type cells.

2015-09-03 | E-GEOD-72638 | biostudies-arrayexpress

Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in three Pseudomonas strains.

2014-05-08 | GSE56856 | GEO

MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently (KT2440)

Project description:MvaT proteins are recognized as a member of H-NS family proteins in pseudomonads. IncP-7 conjugative plasmid pCAR1, which was originally found in Pseudomonas resinovorans, carries an mvaT homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, it was previously reported that pmr and chromosomally-encoded homologous genes, turA and turB, are majorly transcribed, and that Pmr interacts with TurA and TurB in vitro (Yun et al. J. Bacteriol. 192:4720-4731, 2010). In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Modified ChIP-chip analyses suggested that the binding sites of Pmr, TurA, and TurB in P. putida KT2440(pCAR1) genome were almost identical; nevertheless, transcriptome analyses using deletion mutants of each MvaT protein gene at the log and early-stationary growth phases clearly suggested that their regulons were different with one another. Especially, significant dissimilarity of regulons was found between Pmr and other two proteins. Transcriptions of the larger number of genes were affected by Pmr deletion at the early-stationary phase than at the log phase, suggesting that Pmr minimizes the pCAR1 effects on host fitness more effectively at the early-stationary phase. On the other hand, similarity found between the regulons of TurA and TurB implied that they may have complementary roles as global transcriptional regulators in response to the plasmid carriage. ChIP-chip: Pseudomonas putida KT2440 harboring plasmid pCAR1 cells were ChIPed with His-tag (C-terminus of each MvaT homologs) and compared with input control. Transcriptome analysis: Chromosomal RNA maps of mvaT deletion mutants were compared with those of wild-type cells.

2015-09-03 | E-GEOD-72637 | biostudies-arrayexpress

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2)

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.

2018-11-22 | PXD007090 | Pride

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440

2018-09-24 | PXD007089 | Pride

Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440.

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007089.

2018-11-21 | PXD007133 | Pride

Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2).

2018-11-21 | PXD007722 | Pride

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