Structural and Boolean Network Modeling of the Levan Biosynthetic Pathway in Bacillus subtilis

Motivation Levan is a fructose polymer with applications in the creation of hydrogels for drug delivery and wound healing. In industrial biotechnology. Bacillus subtilis is the key organism for producing levan. However, the metabolic models of Bacillus subtilis available do not include the biosynthesis of levan. To understand levan biosynthesis in B. subtilis, we employed structural systems biology integrating known structural details of proteins in the B. subtilis metabolic pathway to create a structure-annotated genome-scale metabolic model (GEM). To fill gaps in structural information about the enzymes, AlphaFold2 was used. Thus, this study enhances the metabolic model of B. subtilis by incorporating the biosynthesis of levan and including structural information about the proteins involved.

The manually curated model links proteins and reactions to protein data bank (PDB) entries, providing structural perspectives previously overlooked in GEMs. We mapped 508 PDB structures to 168 UniProt IDs to unravel 331 out of 1250 reactions (26.5%) in B. subtilis with focused coverage of sacB, sacC, sacX/Y, levD/E/F/G, and sacP. The structural layer does not alter stoichiometry or constraints unless explicitly parameterized. This structure-annotated resource enables the systematic testing of phenotype predictions and design strategies. Our structure-based metabolic model advances the understanding of levan production and microbial metabolism, facilitating sustainable and efficient biotechnological processes for industrial applications. Availability and implementation Data available at the github page (https://github.com/raghuyennamalli/levan_ssbio) Competing Interest Statement The authors have declared no competing interest.