The finding that basically eight of fifteen identified transcripts in the ICEclc core region are upregulated during stationary phase, suggests a coordinated global control mechanism, which is perhaps assisted by the stationary phase sigma factor RpoS. Indeed, some evidence HKI-272 nmr for RpoS control was obtained from sequence motifs in the inrR promoter. It

is interesting to speculate as to what would be the ecological or physiological advantage for ICEclc to become active during stationary phase. One hypothesis is that of the ‘sinking ship’: the element senses that its host survival (and therefore that of itself) is endangered and tries to escape to a more favorable host cell (even though this must be in its immediate vicinity). Even more intriguing is perhaps the carbon substrate-specific upregulation of ICEclc activity, which is highest after growth on 3-chlorobenzoate, less with fructose and very low with glucose or succinate as carbon sources. Upregulation of the ICEclc core region expression in stationary phase cells grown with 3-chlorobenzoate is in agreement

with previous results showing increased activity of the integrase promoter [26], increased proportion of ICEclc excised DNA and increased ICEclc transfer rates [27]. Since it is assumed that during stationary phase cells have depleted their carbon source, the selleck chemicals carbon source can no longer be directly be responsible for the activation, but somehow must have generated a ‘memory’ effect which triggers ICEclc response. In this light, the repression seen for transcription read-through from Sapanisertib concentration ORF101284 with glucose and succinate might point to a Crc-type regulation of catabolite repression in Pseudomonas [32, 33], although for the time being no specific Crc binding motifs were detected in the ICEclc core region. Conclusions In conclusion, we have identified fifteen transcripts covering the presumed core region for behavioral functions of ICEclc. Eight of those are concertedly upregulated during stationary

phase, but only after previous growth of the cells on 3-chlorobenzoate or fructose, which explains previous results that have seen highest ICEclc transfer rates under such conditions [27]. TGF-beta inhibitor The number and lengths of ICEclc transcripts is similar to that found for typical conjugative plasmid systems, yet the mode of global transcription control is more reminiscent for phage-type control. We thus conclude that the hybrid transcriptional control mode comprising both conjugative plasmid and phage strategies has been selected in mobile elements of the ICEclc group. Methods Growth conditions and harvesting P. knackmussii B13, the original host of ICEclc, was cultivated in minimal medium (MM) based on the type 21C medium [34].