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Series GSE10862 Query DataSets for GSE10862
Status Public on Oct 18, 2008
Title High-resolution mapping of the pCAR1 plasmid transcriptomes in Pseudomonas
Platform organism Pseudomonas
Sample organisms Pseudomonas putida; Pseudomonas resinovorans
Experiment type Expression profiling by array
Summary 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.
Contributor(s) Miyakoshi M, Nishida H, Shintani M, Nojiri H
Citation(s) 19134166
Submission date Mar 17, 2008
Last update date Dec 10, 2013
Contact name Masatoshi Miyakoshi
Organization name Tohoku University
Department Department of Environmental Life Sciences
Lab Laboratory of Microbial Genetics
Street address Aoba-ku, Katahira, 2-1-1
City Sendai
State/province Miyagi
ZIP/Postal code 980-8577
Country Japan
Platforms (1)
GPL6591 [pCAR1_8b520435F] Affymetrix CustomExpress IncP-7 plasmid pCAR1 Tiling Array
Samples (4)
GSM275463 CA10_succinate_rep1_and_rep2
GSM275464 CA10_carbazole_rep1_and_rep2
GSM275465 KT2440(pCAR1)_succinate_rep1_and_rep2
BioProject PRJNA107363

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10862_RAW.tar 6.7 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file

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