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

Masatoshi Miyakoshi1, Hiromi Nishida, Masaki Shintani

  • 1Biotechnology Research Center, The University of Tokyo, Tokyo, Japan. mmiyakoshi@ige.tohoku.ac.jp

BMC Genomics
|January 13, 2009
PubMed
Summary

Plasmid gene expression can change based on the bacterial host. This study used tiling arrays to map transcripts of the carbazole catabolic plasmid pCAR1, revealing host-dependent variations in operon transcription levels.

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Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Plasmids are extrachromosomal DNA elements capable of autonomous replication and horizontal gene transfer via conjugation.
  • The influence of host genetic background on plasmid gene expression and resulting phenotypic variation remains underquantified.

Purpose of the Study:

  • To quantitatively investigate the expression range of plasmid genes in different bacterial host backgrounds.
  • To map and quantify transcripts of the carbazole catabolic plasmid pCAR1 in native and transconjugant hosts.

Main Methods:

  • Utilized a high-density (9 bp) tiling microarray for comprehensive transcript mapping.
  • Quantified plasmid pCAR1 transcripts in *Pseudomonas resinovorans* CA10 and *P. putida* KT2440(pCAR1) under different carbon sources (carbazole, succinate).
  • Validated tiling array results with quantitative RT-PCR and primer extension assays.

Main Results:

  • Identified operons within pCAR1, showing largely conserved transcription units across different hosts when grown on the same carbon source.
  • Confirmed upregulation of carbazole degradation operons during growth on carbazole in both hosts.
  • Observed significantly higher transcription levels of operons near the transfer gene cluster in the transconjugant host (*P. putida*) compared to the original host (*P. resinovorans*).

Conclusions:

  • Plasmid operon transcription levels are demonstrably influenced by the bacterial host background.
  • High-resolution tiling arrays are effective for simultaneous identification and quantification of prokaryotic transcriptomes, including operons and non-coding RNAs.