Abstract
BackgroundIntegrative and conjugative elements (ICE) form a diverse group of DNA elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell. ICE come in different families, typically with a conserved core for functions controlling the element's behavior and a variable region providing auxiliary functions to the host. The ICEclc element of Pseudomonas knackmussii strain B13 is representative for a large family of chromosomal islands detected by genome sequencing approaches. It provides the host with the capacity to degrade chloroaromatics and 2-aminophenol.ResultsHere we study the transcriptional organization of the ICEclc core region. By northern hybridizations, reverse-transcriptase polymerase chain reaction (RT-PCR) and Rapid Amplification of cDNA Ends (5'-RACE) fifteen transcripts were mapped in the core region. The occurrence and location of those transcripts were further confirmed by hybridizing labeled cDNA to a semi-tiling micro-array probing both strands of the ICEclc core region. Dot blot and semi-tiling array hybridizations demonstrated most of the core transcripts to be upregulated during stationary phase on 3-chlorobenzoate, but not on succinate or glucose.ConclusionsThe transcription analysis of the ICEclc core region provides detailed insights in the mode of regulatory organization and will help to further understand the complex mode of behavior of this class of mobile elements. We conclude that ICEclc core transcription is concerted at a global level, more reminiscent of a phage program than of plasmid conjugation.
Highlights
Integrative and conjugative elements (ICE) form a diverse group of DNA elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell
Transcriptional organization of the ICEclc core region In order to analyze the transcriptional organization of the core region of ICEclc, we used a combination of conventional molecular techniques and semi-tiling micro-array analyses
The ICEclc core spans the region between nucleotide 50,000 until the left end of the element, and comprises the most conserved stretch among a number of closely related genomic islands' (GEI) [24,26]
Summary
Integrative and conjugative elements (ICE) form a diverse group of DNA elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell. The ICEclc element of Pseudomonas knackmussii strain B13 is representative for a large family of chromosomal islands detected by genome sequencing approaches It provides the host with the capacity to degrade chloroaromatics and 2-aminophenol. A large new class of DNA elements has been recognized that contributes importantly to bacterial genome evolution via horizontal gene transfer. Most of these have been detected by comparative genome sequencing and have in general been named 'genomic islands' (GEI) to portray their foreign character within the host genome [10]. A self-transferable GEI (e.g., ICE, conjugative transposons and other types) can move its excised DNA to a new host, where it can reintegrate with the help of an integrase enzyme at one or more specific insertion sites. Preliminary regulation studies were performed on ICEHin1056 [16] and the Pseudomonas aeruginosa elements pKLC102 and PAGI-2 [19], but without attaining a global level
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