Native characteristics and biotechnological perspectives of fatty acid metabolism and its regulation in Sulfolobus acidocaldarius

Ever since their discovery, archaea and the many extremophiles belonging to this distinct domain of life have piqued interest. From a fundamental point of view, study of archaea has contributed to unraveling the mystery of the origin of life and complex biological systems we find in nature. In addition, study of extremophilic archaea allows us to understand how life at the borders of environmental extremes has adapted to not only survive but thrive in such environments. However, despite decades of research, many biological aspects of extremophilic archaea are still not well characterized. One such example is fatty acid metabolism. Unlike bacteria or eukarya that incorporate fatty acid-based lipids in their membranes, archaea employ isoprenoid-based phospholipids. Nevertheless, although the biological role of fatty acids in these organisms is unknown, archaeal genomes typically encode a large relative fraction of genes involved in fatty acid metabolism.

The abundance of archaea thriving in extreme conditions is interesting from a biotechnological viewpoint as well, given the potential development of more (cost- )efficient industrial processes using these organisms and their enzymes. Fatty acids and their derivatives are considered to be interesting target chemicals for biomanufacturing as a more sustainable alternative for petrochemical production. The consideration of extremophilic archaea and their biological parts as valuable components of biological production processes enforces the necessity to better characterise native mechanisms and metabolisms involving interesting target chemicals like fatty acids.

Sulfolobus acidocaldarius is a thermoacidophilic archaeon that thrives at temperatures between 70-80°C and a pH between 2 and 3. It is an important model organism for the study of (cren)archaea. Its thermophilic and acidophilic characteristics render it an interesting host for industrial (bio)processes. In this PhD project, I aimed to generate a better understanding of fatty acid metabolism and its regulation in S. acidocaldarius, thereby opening perspectives for potential industrial applications. A first focus for the characterization of fatty acid metabolism is a fatty acid and lipid metabolism gene cluster (saci_1103-1126). We investigated potential pathways and functions for these genes by in silico analysis, revealing the presence of esterases, lipases and ß-oxidation enzymes. Furthermore, a TetR transcriptional regulator, FadRSa, located in this gene cluster was extensively characterized. It has two modes of binding dependent on the recognition sequence (dimer or dimer-of-dimer stoichiometry) and is able to regulate the entire gene cluster by only binding a limited number of distinct binding sites in non-canonical positions relative to the operator sequences. Using the knowledge obtained from its characterization, several hybrid bacterial promoters regulated by the archaeal FadRSa were constructed and characterized. This allows us to better understand the regulatory mechanisms employed by FadRSa and takes the first steps towards expanding the available acyl-CoA responsive promoters. Finally, predicted ßoxidation enzymes from members of the Sulfolobales were purified and characterized, taking the first steps towards better understanding of fatty acid metabolism in these organisms and simultaneously identifying interesting enzymes that could be used in engineering strategies.