Integrated analysis of gene expression, protein synthesis, and epigenetic modifications in alcanivorax borkumensis SK2 under iron limitation

Abstract

This study aimed to understand the genetic and molecular mechanisms enabling Alcanivorax borkumensis SK2, a hydrocarbonoclastic marine bacterium, to thrive under iron-limited conditions. Using SMRT PacBio whole-genome sequencing, Illumina total RNA sequencing, and proteomics analysis, we examined the strain's response to iron-rich and iron-depleted media. Despite minimal impact on growth, significant changes in gene expression were observed when using n-tetradecane or acetate under iron limitation. Iron scarcity, depending on the carbon source, affects energy metabolism, membrane transport, lipid metabolism, stress-adaptive responses, and siderophore synthesis. We identified several methyltransferases (MTases) in the studied genome, including RS14230, which is a part of a fully functional restriction-modification (RM) system causing bipartite cytosine methylation and DNA cleavage at AgGCcT sites. Another MTase, RS09425, controls bipartite adenine methylation at GaTNNNNNGtGG motifs; however, no restriction activity at these motifs has been detected. Many epigenetically modified nucleotides lacked canonical motifs, possibly due to MTase byproducts. Notably, non-canonical modifications were statistically associated with transcriptional start sites and gene regulation, suggesting an indirect role in transcription via DNA conformation changes and its accessibility to MTases near actively transcribed genes.