Divalent cations promote the transfer of the IncP-7 plasmid pCAR1 among different Pseudomonas hosts
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE97565
PROVIDER: PRJNA382324 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:An incompatibility P-7 plasmid pCAR1 can be efficiently transferred among artificial microcosms in the presence of divalent cations Ca2+ and Mg2+. One on one mating assays between Pseudomonas strains with different plasmids showed that the promotion of transfer efficiency by divalent cations was also found in other plasmids including pB10 and NAH7, whereas the impacts were larger in IncP-7 plasmids. The impact on pCAR1 transfer altered by different pairs of donor and recipient strains, and the promotion of transfer efficiency was clearly detected between donors P. resinovorans CA10dm4 and P. fluorescens Pf0-1 to the recipients P. putida KT2440 and CA10dm4. Transcriptome analyses showed that genes on the pCAR1 did not respond to the presence of cations, including the tra/trh genes involved in its transfer. Notably, transcriptions of oprH genes, encoding a putative outer membrane proteins, in both of donor and recipient were commonly upregulated under the cation-limited condition. Transfer frequency of the pCAR1 to the transposon mutant of oprH in KT2440 was not promoted by the cations. This effect was partially recovered by the complementation with oprH gene, suggesting that OprH is involved in the promotion the pCAR1 transfer by divalent cations.
2017-04-11 | GSE97565 | GEO
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
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.
2015-09-03 | GSE72638 | GEO
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
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
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.
2015-09-03 | GSE72637 | GEO
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
Project description:Nucleoid-associated proteins (NAPs) are known to fold bacterial DNA and influence global transcription. Incompatibility P-7 plasmid pCAR1 carries three genes encoding NAPs: H-NS family protein Pmr, NdpA-like protein Pnd, and HU-like protein Phu. Because previous reports about plasmid-encoded NAPs mainly focused on H-NS homologs, functions and importance of different kinds of NAPs encoded on a plasmid remained unknown. Here, we assessed the effects of single or double disruption of pmr, pnd, and phu in a host P. putida KT2440. When pmr and pnd or pmr and phu were disrupted simultaneously, stability and conjugation frequency of pCAR1 decreased significantly. In the comprehensive phenotypes comparisons, host availabilities of some compounds, which were reduced by pCAR1carriage, were restored by NAP-gene(s)-disruption. Transcriptome analyses showed that Pmr and Pnd have different regulons, whereas Phu mainly supports their gene regulation. These cooperative functions of the three NAPs were not simply due to protein-protein interactions because hetero-oligomers of them were not detected in pull-down assays. Our present study is the first report about the cooperative function of plasmid-encoded different kinds of NAPs, which show no homology with each other.
2013-12-07 | GSE53068 | GEO
Project description:Impacts of plasmid carriage on its host cell were comprehensively analyzed using conjugative plasmid pCAR1 in the three different kinds of hosts, Pseudomonas putida KT2440, P. aeruginosa PAO1, and P. fluorescens Pf0-1. Various analyses of the host phenotype showed that pCAR1 carriage reduced host fitness, swimming motility, and resistances to osmotic- or pH-stress, and brought about the alterations of primary metabolic capacities in the TCA cycle or those several steps away from the TCA cycle in the host cells. Growth phase-dependent transcriptome analyses were performed with the classification of the annotated genes based on their identities among the three hosts and their putative functions. pCAR1 carriage affected host transcriptome more greatly at the transition and stationary phases in each host. The transcriptome responses were more similar between KT2440 and PAO1 than between other host combinations, and many genes, such as for ribosomal proteins, F-type ATPase, and RNAP core, in both strains were commonly not suppressed in their stationary phases. These responses may have resulted in the reduction of host fitness, motility, and stress resistances. Host-specific responses to plasmid carriage were transcriptional changes of genes on putative prophage or foreign DNA regions. The extent of the impacts in host phenotypes and transcriptomes was similarly the largest in KT2440 and the lowest in Pf0-1. The host alterations controlled by pCAR1 carriage are important for understanding the fate of the plasmid and its host, plasmid maintenance, expression of plasmid genes, the host cell physiology, and host survivability in the environment. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring KT2440 and non-pCAR1 harboring KT2440 were compared. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring PAO1 and non-pCAR1 harboring PAO1 were compared. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring Pf0-1 and non-pCAR1 harboring Pf0-1 were compared. The growth-dependent change of RNA maps from exponential to early stationary phases of plasmid pCAR1possessed by 3 kinds of hosts were compared.
2012-12-25 | E-GEOD-39636 | biostudies-arrayexpress
Project description:Impacts of plasmid carriage on its host cell were comprehensively analyzed using conjugative plasmid pCAR1 in the three different kinds of hosts, Pseudomonas putida KT2440, P. aeruginosa PAO1, and P. fluorescens Pf0-1. Various analyses of the host phenotype showed that pCAR1 carriage reduced host fitness, swimming motility, and resistances to osmotic- or pH-stress, and brought about the alterations of primary metabolic capacities in the TCA cycle or those several steps away from the TCA cycle in the host cells. Growth phase-dependent transcriptome analyses were performed with the classification of the annotated genes based on their identities among the three hosts and their putative functions. pCAR1 carriage affected host transcriptome more greatly at the transition and stationary phases in each host. The transcriptome responses were more similar between KT2440 and PAO1 than between other host combinations, and many genes, such as for ribosomal proteins, F-type ATPase, and RNAP core, in both strains were commonly not suppressed in their stationary phases. These responses may have resulted in the reduction of host fitness, motility, and stress resistances. Host-specific responses to plasmid carriage were transcriptional changes of genes on putative prophage or foreign DNA regions. The extent of the impacts in host phenotypes and transcriptomes was similarly the largest in KT2440 and the lowest in Pf0-1. The host alterations controlled by pCAR1 carriage are important for understanding the fate of the plasmid and its host, plasmid maintenance, expression of plasmid genes, the host cell physiology, and host survivability in the environment.
2012-12-25 | GSE39636 | GEO