Fatty acid metabolism in Sulfolobus acidocaldarius

Archaea synthesize membranes using isoprenoid-based ether lipids, while Bacteria and Eukarya use fatty acid-based ester lipids. Despite these differences, some studies have suggested that fatty acids are present in a few Archaea, such as Sulfolobus spp. (1, 2). Furthermore, several archaeal genomes encode complete sets of bacterial-like β oxidation homologues and few archaeal species were found to degrade fatty acids (1, 3). However, no studies to date have been able to fully elucidate the fatty acid metabolism in archaeal species. Here, we address this open question by investigating fatty acid degradation in the archaeal model organisms Sulfolobus acidocaldarius by biochemical characterization and in vitro pathway reconstitution. This work shows that a set of β oxidation homologues present in S. acidocaldarius constitute a functional fatty acid degradation pathway. This pathway involves the sequential activities of an acyl-CoA dehydrogenase (Saci_1123), a bifunctional 3(S)-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase fusion protein (Saci_1109) and β-ketothiolase (Saci_1114) in addition to an unusual fused archaeal electron transfer flavoprotein (Saci_0315). All four proteins were reconstituted in vitro to a complete and fully functional β oxidation cascade that catalyzed the complete degradation of medium chain fatty acid to acetyl-CoA with a pronounced specificity for NAD⁺ and the (S)-hydroxyacyl-CoA stereoisomers. Importantly, a detailed characterization of these enzymes also supports that several mechanistic, specificity and thermodynamic constraints prevent this pathway from functioning in the reverse direction to support fatty acid synthesis. Instead, we propose the presence of a novel fatty acid synthesis pathway in S. acidocaldarius consisting of a β-ketothiolase (Saci_1121), ketoacyl-CoA reductase (Saci_1104), and hydroxyacyl-CoA dehydratase (Saci_1085) that form a stable assembly mediated by a DUF35 domain protein (Saci_1120), while the final step is catalysed by an NADPH-dependent enoyl-CoA reductase (Saci_1115). In summary our study demonstrates that Archaea are capable of synthesizing and degrading fatty acids and elucidates the molecular mechanisms involved in these processes.

[1] D. V. Dibrova et al., Environmental microbiology 16, 907-918 (2014)

[2] T. Hamerly et al., Archaea 2015, 9 (2015)

[3] K. Wang et al., Nature communications 10, 1542 (2019).