Transcriptomics,Genomics

Dataset Information

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High-resolution mapping of the pCAR1 plasmid transcriptomes in Pseudomonas


ABSTRACT: 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 Overall design: We analyzed the plasmid transcriptomes in two strains, Pseudomonas resinovorans CA10 and Pseudomonas putida KT2440(pCAR1), during growth on succinate and carbazole as the sole sources of carbon using the pCAR1 tiling array. We conducted two independent biological replicates for each strain and growth condition.

INSTRUMENT(S): [pCAR1_8b520435F] Affymetrix CustomExpress IncP-7 plasmid pCAR1 Tiling Array

SUBMITTER: Masatoshi Miyakoshi  

PROVIDER: GSE10862 | GEO | 2008-10-18

SECONDARY ACCESSION(S): PRJNA107363

REPOSITORIES: GEO

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Publications

High-resolution mapping of plasmid transcriptomes in different host bacteria.

Miyakoshi Masatoshi M   Nishida Hiromi H   Shintani Masaki M   Yamane Hisakazu H   Nojiri Hideaki H  

BMC Genomics 20090109


BACKGROUND: Plasmids are extrachromosomal elements that replicate autonomously, and many can be transmitted between bacterial cells through conjugation. Although the transcription pattern of genes on a plasmid can be altered by a change in host background, the expression range of plasmid genes that will result in phenotypic variation has not been quantitatively investigated. RESULTS: Using a microarray with evenly tiled probes at a density of 9 bp, we mapped and quantified the transcripts of the  ...[more]

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