Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis

Aconitase, an essential enzyme of the tricarboxylic acid cycle (TCA), so far has been identified only in a minority of archaeal genomes. This enzyme belongs to the aconitase A family, which is represented in most bacteria and eukaryotes. Using iterative sequence database search, we linked two previously uncharacterized protein families (COG1679 and COG1786), respectively, to the three Fe-S-cluster-associated aconitase domains and the swiveling domain, the four domains that are present in all known aconitase families. The respective genes are often found in one predicted operon and, moreover, are fused in several species, suggesting a functional and physical interaction. We predict that these proteins together comprise a previously undetected, distinct aconitase family, which we designated aconitase X. Aconitase X is encoded in the genomes of many archaea and some proteobacteria. Among archaea, the pattern of aconitase X occurrence complements that of aconitase A such that together the two enzymes account for aconitase activity in all archaea. Phylogenetic analysis indicates that aconitase X is likely to be the ancestral archaeal form, with non-orthologous displacement in some of the archaea apparently brought about by horizontal transfer of the gene for bacterial aconitase A. The prediction of aconitase X completes the TCA cycle for Methanothermobacter thermoautotrophicus and Archaeoglobus fulgidus and suggests that most archaea have a full TCA cycle.