Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification

In this study, we employed a multi-omics approach to study the ability of Aspergillus parasiticus MM36, an isolate derived from Tenebrio molitor intestines, to metabolize long-chain alkanes (lcAlk) and secrete enzymes able to modify polyethylene (PE). Following genome sequencing, assembly, and annotation the fungus was grown with hexadecane (C16) or a mixture of long-chain alkanesl (C24 to C36) as carbon sources and secretomes were tested for their ability to modify PE to select timepoints for the multi-omics analysis. The selected conditions were lcAlk after days 2 and 3 and C16 after day 3. Transcriptomic analysis comparing lcAlk to C16 cultures highlighted the enrichment of oxidoreductase activities and carboxylic acid metabolism in both lcAlk days, with transmembrane transporters and transferases predominating on day 2 and biosynthetic processes on day 3. In C16 cultures, hydrolytic enzymes, including esterases, were upregulated alongside Baeyer-Villiger monooxygenases, suggesting a shift toward sub-terminal hydroxylation. Integrating transcriptomic and secretomic data, we propose a mechanism for lcAlk assimilation by A. parasiticus MM36, involving extracellular oxyfunctionalization, hydrocarbon uptake via surface-modifying proteins and channeling through membrane transporters for energy consumption and biosynthesic processes. Overall design: Aspergillus parasiticus MM36 was grown in liquid cultures using mineral medium either supplemented with hexadecane (C16) or a mixture of long-chain alkanes (lcAlk), ranging from C24 to C36, dissolved in hexadecane. Three different conditions were chosen based on the ability of A. parasiticus MM36 secretomes to modify low density polyethylene structure over time. These conditions include hexadecane cultures after 3 days and lcAlk cultures after 2 and 3 days. We conducted RNA-seq at the three conditions in triplicates, however one hexadecane sample with a RIN value of 3.7 was discarded leaving this condition with two replicates.