Halophilic archaea produce wax esters and use an alternative fatty acyl-CoA reductase for precursor synthesis

Wax esters are fatty acid-based neutral lipids thought to be restricted to bacteria and eukaryotes that play a key role in the functioning and maintenance of cells, especially under adverse conditions. Here we show that several halophilic archaea (Halobacteriales) carry a homologue of the bacterial wax synthase gene. Wax ester synthesis and accumulation is demonstrated in one of these (poly)extremophilic archaea, Natronomonas pharaonis, during growth on long-chain fatty acids. Our bioinformatic analysis also shows that the synthesis of fatty alcohols required for wax ester synthesis could be performed by an enzyme evolutionarily related to class I 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, classically involved in isoprenoid biosynthesis). Using heterologous expression and enzymatic assays, we show that this HMGR homolog, which we named FcrA (for fatty acyl-CoA reductase), reduces fatty acyl-CoA to fatty alcohol, but cannot reduce 3-hydroxy-3-methylglutaryl-CoA to mevalonate. The conservation of HMGR catalytic residues in FcrA suggests that the two enzymes have a similar catalytic mechanism, whereas an elongated substrate-binding pocket and distinct residues may explain FcrA’s selectivity for long chain fatty acyl-CoA. In addition to archaea, FcrA is present in a wide range of bacteria, including ~25% of those predicted to produce wax esters, and accounts for a large proportion of the fatty acyl-CoA reductases found in various environments. Challenging the long-held paradigm that archaea cannot biosynthesize fatty acid-based neutral lipids de novo, this study lays the foundations for further physiological, ecological, and biotechnological investigation of neutral lipid production by systems markedly different from those of eukaryotes and bacteria.