Metabolic engineering in Hot Acid: Strategies enabling chemolithotrophy in thermoacidophilic archaea

Abstract

A genome-scale metabolic model was developed to explore metabolic engineering strategies for thermoacidophilic archaea, with a focus on the genetically tractable Sulfolobus acidocaldarius (T_opt 75 °C, pH_opt 2.5). S. acidocaldarius is natively neither an autotroph nor a sulfur oxidizer, although its genome suggests that this might have been the case at some evolutionary point. Comparative genomics provided insights into key genes and pathways missing from S. acidocaldarius necessary for chemolithotrophy. Growth data for the chemolithotrophic sulfur oxidizer, Sulfurisphaera ohwakuensis (T_opt 85 °C, pH_opt 2.0), provided metabolic data to inform model development. Previous metabolic engineering efforts enabled sulfur oxidation by S. acidocaldarius, albeit at levels below native sulfur oxidizers. Model analysis pointed to active sulfur transport as a key missing complement to passive diffusion. Modelling results predicted that sulfur oxidation could drive production of a bio-based chemical, acetone, in engineered strains of S. acidocaldarius with concomitant fixation of CO₂ into product via the 3-Hydroxybutyrate/4-Hydroxybutyrate cycle. The findings here provide new insights into the basis for thermoacidophile chemolithotrophy and motivate further efforts to develop S. acidocaldarius into a valuable metabolic engineering platform.