Transcriptional network between pCAR1 and KT2440 chromosome

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 We conducted two independent microarray experiments (biological replicates) for each strain in exponential phase of growth. We compared three sets of strains or growth conditions; KT2440(pCAR1) at growth with carbazole vs. KT2440(pCAR1) at growth with succinate, KT2440(pCAR1) at growth with succinate vs. KT2440 at growth with succinate, and KT2440(pCAR1) at growth with succinate vs. KT2440(pCAR1deltaORF70) at growth with succinate. We calculated the fold change as the ratio between signal averages of two controls and two treatments.