Characterization of protein interaction surface on fatty acyl selectivity of starter condensation domain in lipopeptide biosynthesis

Engineering of the start condensation domain with improved N-decanoyl catalytic activity for daptomycin biosynthesis

Daptomycin, a lipopeptide comprising an N-decanoyl fatty acyl chain and a peptide core, is used clinically as an antimicrobial agent. The start condensation domain (dptC1) is an enzyme that catalyzes the lipoinitiation step of the daptomycin synthesis. In this study, we integrated enzymology, protein engineering, and computer simulation to study the substrate selectivity of the start condensation domain (dptC1) and to screen mutants with improved activity for decanoyl loading. Through molecular docking and computer simulation, the fatty acyl substrate channel and the protein-protein interaction interface of dptC1 are analyzed. Key residues at the protein-protein interface between dptC1 and the acyl carrier were mutated, and a single-point mutant showed more than three-folds improved catalytic efficiency of the target n-decanoyl substrate in comparing with the wild type. Moreover, molecular dynamics simulations suggested that mutants with increased catalytic activity may correlated with a more "open" and contracted substrate binding channel. Our work provides a new perspective for the elucidation of lipopeptide natural products biosynthesis, and also provides new resources to enrich its diversity and optimize the production of important components.

Construct a synthetic Entner-Doudoroff pathway in Bacillus licheniformis for enhancing lichenysin production

Lichenysin, a cyclic lipopeptide biosurfactant produced by Bacillus licheniformis, is composed of aspartate, glutamine, valine, leucine, isoleucine, and branched chain fatty acids. The synthesis of these amino acids and fatty acids requires pyruvate and NADPH as the primary precursor and cofactor. Therefore, a sufficient supply of pyruvate and NADPH is crucial for lichenysin production. This study aimed to increase lichenysin production by constructing a synthetic ED pathway in B. licheniformis WX02 through introducing phosphogluconate dehydratase (encoded by gene edd) and 2-keto-3-deoxygluconate 6-phosphate aldolase (encoded by gene eda) from Escherichia coli. Additionally, the NADP⁺-dependent glucose-6-phosphate dehydrogenase (encoded by gene zwf) was overexpressed, resulting in an engineered strain WX02/pHY-edda(Ec)-zwf. Analysis of the fermentation process revealed that the concentrations of pyruvate, aspartate, glutamine, valine, leucine, branched-chain fatty acids (iC15:0, aC15:0, iC16:0, iC17:0), and NADPH in WX02/pHY-edda(Ec)-zwf were increased by 77.21%, 80.41%, 85.31%, 141.64%, 44.94%, 35.08%, 38.08%, 19.33%, 21.16%, and 425%, respectively, compared to the control strain WX02/pHY300, which resulted in a 45.43% increase of lichenysin titer. This work took advantage of the ED pathway to increase lichenysin production for the first time, and provides a promising strategy for boosting the productivity of biochemicals that require pyruvate and NADPH as precursor and cofactor.

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.