Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis

Abstract

Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C16–C30, in Af3–Af5 and C16–C24 in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.

Characterization of the Mycoremediation of n-Alkanes and Branched-Chain Alkanes by Filamentous Fungi from Oil-Polluted Soil Samples in Kazakhstan

“…Depending on the chain length of the substrate, different enzymes could be integrated into the process; C 1 –C 4 are known to be oxidized by the methane monooxygenase and C 5 to C 16 by alkane hydroxylases or cytochrome P450 monooxygenases [ 16 ]. Recently, Aspergillus flavus monooxygenases have been identified as potential bricks in the degradation of long-chain alkanes (>C 16 ; [ 44 ]). The genus Penicillium isolated from oil-contaminated soil has been described as the most active oil degrader [ 45 , 46 , 47 ].…”

Bioremediation of petroleum hydrocarbon contaminated soil: a review on principles, degradation mechanisms, and advancements

“…Degradation catabolism of alkanes is initiated by oxygenases, which introduce oxygen atoms into n-alkanes via four different pathways. The terminal oxidation pathway involves oxidation of the n-alkane terminal methyl group (Perera et al, 2022). The products of oxidation are primary alcohols, which are further oxidized to fatty acids by alcohol and aldehyde dehydrogenases, and then undergo β-oxidation (Fordwour et al, 2018).…”