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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. CONCLUSION: 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.

SUBMITTER: Miyakoshi M

PROVIDER: S-EPMC2642839 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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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

<h4>Background</h4>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.<h4>Results</h4>Using a microarray with evenly tiled probes at a density of 9 bp, we mapped and quantified the trans ...[more]

PMID: 19134166

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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.

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

Publications

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

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