This alkane-induced protein would thus be a prime candidate potentially mediating alkane transport. Using a transcriptomics approach, a number of additional alkane-induced regulatory systems have been detected (Table 1), as compared with our previous proteomics study (Sabirova et al., 2006). A transcriptional regulator of the GntR family, ALK inhibitor encoded by ABO_0121, is located next to the ABO_0122 encoding the alkB2 monooxygenase, suggesting that the ABO_0121-encoded gene product might regulate the expression of the adjacent monooxygenase. Another regulatory system consisting of ABO_1708 and
ABO_1709, adjacent to each other and likely to be operon-arranged, encodes a pair of sensor histidine kinase and DNA-binding response regulator that are also upregulated on alkanes. Their close proximity to the gene of fatty acid degradation (fadH dienoyl-CoA reductase) may indicate that this regulatory system controls the oxidation of fatty acids in Alcanivorax. Our transcriptome data also hint towards quorum sensing playing a role in biofilm formation of Alcanivorax on alkanes, as the major transcriptional
regulator QseB encoded by ABO_0031 was found to be upregulated on hexadecane (Table 1). Quorum sensing has indeed been reported to trigger biofilm formation via the biosynthesis of extracellular exopolysaccharides (EPS) (Sauer et al., 2002), also visible on our EM pictures. We did not detect increased expression
of the cognate histidine kinase, QseC, encoded by ABO_0030. This finding indicates that for initial signal reception and transduction constant levels of sensor Ribociclib protein suffice, while the subsequent coordinated regulation of the expanded quorum-sensing regulon qse does require increased titers of Qse regulator protein. Finally, an HD-GYP domain protein encoded by ABO_2132 and mentioned earlier in ‘Alkane-induced biofilm formation and adhesion to hydrocarbons’ is also upregulated on alkanes and hence represents Phosphoprotein phosphatase another worthy target for regulatory studies of growth on alkanes. To conclude, our transcriptomics analysis of A. borkumensis responses to alkane exposure adds a complementary view on alkane metabolism by this bacterium, in addition to our previous proteomics study, and reveals a number of novel observations, for instance concerning the molecular mechanisms of alkane transport across the cytoplasmic membrane, and pointing to a diverse set of enzymes for the degradation of alkanes. Alcanivorax SK2 seems to respond to growth on alkanes by forming cell aggregates, probably supported by enhanced synthesis of EPS and probably following in a quorum-sensing-mediated aggregation process. Finally, the study has also revealed many transcriptional regulators to be differentially expressed, indicating a complex regulatory interplay of alkane degradation with other metabolic functions in this marine organism.