Bioinformatics analysis and molecular cloning of squalene synthase from Simaroubaceae

Quassinoids are a class of highly oxygenated triterpenoids with C-18, C-19, C-20, C-22, or C-25 skeletons. Squalene synthase (SQS), a key enzyme in the quassinoids biosynthetic pathway, serves as the first step in controlling carbon flux flow into downstream quassinoids. In this study, we screened and analyzed the SQSs from the transcriptome data of the Simaroubaceae family, including AaSQS, BjSQS, AeSQS, QaSQS, ElSQS, and SaSQS. Bioinformatics analysis showed that these SQSs contain C-terminal transmembrane regions and exhibit over 80 % sequence identity with that of Glycyrrhiza glabra (GgSQS1). Phylogenetic analysis revealed that the SQSs from the Simaroubaceae family are more closely related to Malus domestica and Crataegus pinnatifida within the Rosales clade, suggesting an evolutionary trajectory that corroborates the taxonomic classification of Simaroubaceae within the Rosanae superorder. To characterize the function of the SQS from the Simaroubaceae family, the full-length AaSQS was cloned. A soluble AaSQS was obtained by expressing the truncated version lacking 24 amino acids at the C-terminal region in Escherichia coli. Functional analysis showed that AaSQS could catalyze the production of squalene from farnesyl pyrophosphate (FPP). Structural prediction and molecular docking indicated that residues S50, F51, L205, N209, R212, C286, P289, and M313 may be key catalytic residues in AaSQS. Further mutation analysis revealed that all mutants except C286A showed reduced squalene accumulation compared to the wild type (WT). These results provide guidance for quassinoid biosynthesis through metabolic engineering and synthetic biology strategies, particularly by engineering key amino acid residues to enhance enzymatic activity. This study advances the understanding of SQSs in the Simaroubaceae family and provides an important foundation for the study of quassinoid biosynthesis.