Prophage 2 of strain activator Ivacaftor T5T is a Mu-like bacteriophage, not present in strain DSM 17395. It was previously shown that strain T5T produces two different AHLs, i.e. C18-en-HSL and N-3-hydroxydecanoyl-homoserine lactone (3OHC10-HSL) . In P. inhibens strain DSM 17395 TDA and pigment production are regulated via a pgaR-pgaI QS system . The AHL synthase encoding gene pgaI in DSM 17395 is responsible for the production of 3OHC10-HSL. In the genome of strain T5T we found a homologous system probably coding for the 3OHC10-HSL producing AHL synthase (Inhi_2120, homolog to pgaI) and the respective regulator (Inhi_2121, homologous to pgaR) (Figure 3, QS system I). Thus TDA production in strain T5T might also be regulated by a QS system. In addition, two further QS systems (QS system II and III; Figure 3) were found on the chromosome of T5T.
System II is formed by the genes Inhi_0506 and _0507 and is located in the prophage region 2. Orthologs for these QS system genes are also present in P. inhibens strain DSM 24588 (PGA2_c18960 and PGA2_c18970) but absent in strain DSM 17395. QS system III consists of the genes Inhi_1819 and _1820 and is unique for strain T5T compared to P. inhibens DSM 17395 and DSM 24588. It is also located in the potential prophage 1 region (Fig. 3). A homologous system was found in the genome of Phaeobacter caeruleus DSM 24564T and the neighboring genes show a high synteny. The location in the prophage region and the high synteny to the system of P. caeruleus suggest a possible gene transfer of this QS system via a bacteriophage.
The functions of QS system II and III are currently unknown, but it is likely that the compound C18-en-HSL is produced by one of those systems. Two functions were suggested that can possibly be used as unique chemotaxonomic markers for the species P. inhibens within the Roseobacter clade . The genes coding for the first of these functions are located on the chromosome and are involved in cell wall development and surface attachment [dltA encoding a D-alanine-poly(phosphoribitol) ligase involved in biosynthesis of D-alanyl-lipoteichoic acid]. The second unique function is the biosynthesis and transport of iron-chelating siderophores, and the encoding genes are located on the plasmid pPGA1_78 and pPGA2_95, respectively. These two clusters are also present in the genome of strain T5T.
The siderophore gene cluster (Inhi_3924 �C Inhi_3928) is located on the 78 kb plasmid (Fig. 3) and the dltA gene cluster (Inhi_1065 – Inhi_1086) is located on the chromosome (Fig. 3). Screenings in the newly available Roseobacter genomes showed that Leisingera methylohalidivorans DSM 14336  and Leisingera aquimarina DSM 24565  also harbor the genes for siderophore synthesis. The uniqueness of the dltA gene cluster within Batimastat the species P. inhibens, however, remains and can be used as chemotaxonomic marker.