Epigenetic regulation in Alcanivorax borkumensis in response to environmental stresses.

A. borkumensis SK2 is a cosmopolitan hydrocarbonoclastic marine bacterium with an specialized metabolism strictly dependent on iron availability. The aim of this study was to investigate the ability of A. borkumensis SK2 to cope with iron-limiting conditions when grown on different carbon sources. Methylomic rearrangement and its impact on transcriptomic and proteomic responses was examined. Our findings indicated that A. borkumensis SK2 growth is not significantly impacted by iron deficiency, regardless of the carbon source utilized (n-tetradecane or acetate). However, notable alterations were observed in the transcriptomic profile when using any of these carbon sources. Overexpression of genes associated with various metabolic pathways, especially those related to iron uptake and siderophore synthesis, was observed in iron deficiency conditions with acetate. In contrast, only enzymes involved in a key metabolic pathway like (ATP biosynthesis and acyl-CoA metabolic process, nucleic acid biosynthesis process, amino acid and protein synthesis exhibited overexpression with tetradecane. Our study shows that methylation at the promoter and gene levels is associated with changes in genomic expression. The number of genes overexpressed among those with higher methylation levels increased significantly, regardless of the carbon source tested. Regarding iron metabolism, the two types of siderophores in Alcanivorax exhibited differential expression patterns. Genes encoding amphiphilic type siderophores were found to be overexpressed when acetate was used as the carbon source. However, when tetradecane was used, these genes were not found to be differentially expressed, altough the corresponding proteins were overexpressed, indicating the necessity to scavenge deficient iron molecules. Using both substrates, these genes were found to be more methylated than the gene encoding the pseudomonine-like siderophore. The observation of overexpression of the corresponding protein in the presence of tetradecane suggests a potential epigenetic role in the post-transcriptional regulation for this specific siderophore.