title: High-resolution mapping of plasmid transcriptomes in different host bacteria.
abstract: 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 carbazole catabolic plasmid pCAR1 in its original host Pseudomonas resinovorans CA10 and the transconjugant P. putida KT2440(pCAR1) during growth on either carbazole or succinate as the sole carbon source. We identified the operons in pCAR1, which consisted of nearly identical transcription units despite the difference in host background during growth on the same carbon source. In accordance with previous studies, the catabolic operons for carbazole degradation were upregulated during growth on carbazole in both hosts. However, our tiling array results also showed that several operons flanking the transfer gene cluster were transcribed at significantly higher levels in the transconjugant than in the original host. The number of transcripts and the positions of the transcription start sites agreed with our quantitative RT-PCR and primer extension results.
  
  
  CONCLUSIONS
  Our tiling array results indicate that the levels of transcription for the operons on a plasmid can vary by host background. High-resolution mapping using an unbiased tiling array is a valuable tool for the simultaneous identification and quantification of prokaryotic transcriptomes including polycistronic operons and non-coding RNAs.
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Tokyo, Japan. mmiyakoshi@ige.tohoku.ac.jp
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Miyakoshi
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nishida
authors.forename: Masaki
authors.initials: M
authors.lastname: Shintani
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Yamane
authors.forename: Hideaki
authors.initials: H
authors.lastname: Nojiri
mesh_terms: D002227:Carbazoles / Q000378:metabolism; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D010957:Plasmids / Q000235:genetics*; D011549:Pseudomonas / Q000235:genetics* / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D002227:Carbazoles; D012329:RNA, Bacterial; C041514:carbazole