Biosynthesis of isoprenoids via mevalonate in archaea: The lost pathway

Isoprenoid compounds are ubiquitous in living species and diverse in biolog ical function. Isoprenoid side chains of the membrane lipids are biochemica l markers distinguishing archaea From the rest of living forms. The mevalon ate pathway of isoprenoid biosynthesis has been defined completely in yeast , while the alternative, deoxy-D-xylulose phosphate synthase pathway is Fou nd in many bacteria. In archaea, some enzymes of the mevalonate pathway are found, but the orthologs of three yeast proteins, accounting for the route from phosphomevalonate to geranyl pyrophosphate, are missing, as are the e nzymes from the alternative pathway. To understand the evolution of isopren oid biosynthesis, as well as the mechanism of lipid biosynthesis in archaea , sequence motifs in the known enzymes of the two pathways of isoprenoid bi osynthesis were analyzed. New sequence relationships were detected, includi ng similarities between diphosphomevalonate decarboxylase and kinases of th e galactokinase superfamily, between the metazoan phosphomevalonate kinase and the nucleoside monophosphate kinase superfamily, and between isopenteny l pyrophosphate isomerases and MutT pyrophosphohydrolases. Based on these f indings, orphan members of the galactokinase, nucleoside monophosphate kina se, and pyrophosphohydrolase families in archaeal genomes were evaluated as candidate enzymes far the three missing steps. Alternative methods of find ing these missing links were explored, including physical linkage of open r eading frames and patterns of ortholog distribution in different species. C ombining these approaches resulted in the generation of a short list of 13 candidate genes for the three missing functions in archaea, whose participa tion in isoprenoid biosynthesis is amenable to biochemical and genetic inve stigation.