title: Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Fundamental Microbiology, University of Lausanne, Switzerland.
authors.forename: Muriel
authors.initials: M
authors.lastname: Gaillard
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pradervand
authors.forename: Marco
authors.initials: M
authors.lastname: Minoia
authors.forename: Vladimir
authors.initials: V
authors.lastname: Sentchilo
authors.forename: David R
authors.initials: DR
authors.lastname: Johnson
authors.forename: Jan Roelof
authors.initials: JR
authors.lastname: van der Meer
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D004251:DNA Transposable Elements / Q000235:genetics* / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D042822:Genomic Instability; D044404:Genomic Islands; D020411:Oligonucleotide Array Sequence Analysis; D011549:Pseudomonas / Q000235:genetics* / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements