A unique fungal lysine biosynthesis enzyme shares a common ancestor with tricarboxylic acid cycle and leucine biosynthetic enzymes found in diverse organisms

Abstract

Fungi have evolved a unique alpha-amino-adipate pathway for lysine biosynthesis. The fungal-specific enzyme homoaconitate hydratase from this pathway is moderately similar to the aconitase-family proteins from a diverse array of taxonomic groups, which have varying modes of obtaining lysine. We have used the similarity of homoaconitate hydratase to isopropylmalate isomerase (serving in leucine biosynthesis), aconitase (from the tricarboxylic acid cycle), and iron-responsive element binding proteins (cytosolic aconitase) from fungi and other eukaryotes, eubacteria, and archaea to evaluate possible evolutionary scenarios for the origin of this pathway. Refined sequence alignments show that aconitase active site residues are highly conserved in each of the enzymes, and intervening sequence sites are quite dissimilar. This pattern suggests strong purifying selection has acted to preserve the aconitase active site residues for a common catalytic mechanism; numerous other substitutions occur due to adaptive evolution or simply lack of functional constraint. We hypothesize that the similarities are the remnants of an ancestral gene duplication, which may not have occurred within the fungal lineage. Maximum likelihood, neighbor joining, and maximum parsimony phylogenetic comparisons show that the alpha-aminoadipate pathway enzyme is an outgroup to all aconitase family proteins for which sequence is currently available.

A Developmentally Regulated Aconitase Related to Iron-regulatory Protein-1 Is Localized in the Cytoplasm and in the Mitochondrion of Trypanosoma brucei

“…4). The general topology of the tree is very similar to published trees of the aconitase family (53,57,58). TbACO is clearly separated from the mitochondrial aconitases.…”

Role of Saccharomyces cerevisiae ISA1and ISA2 in Iron Homeostasis

“…By comparison, the lysine growth requirement of isa⌬ strains cannot be explained by a similar aconitase deficiency, since yeast aco1 mutants are not lysine auxotrophs. The lysine biosynthetic pathway in yeast utilizes a single Fe-S enzyme, a fungal specific [4Fe-4S] homoaconitase presumed to be mitochondrial in location (18,47,51). Although it was not possible to obtain comparative measurements of homoaconitase activity, a defect in this enzyme is a likely cause of the lysine auxotrophy.…”

Characterization of a lysK gene as an argE homolog in Thermus thermophilus HB27

“…One is the diaminopimelate (DAP) pathway starting from aspartate via DAP, as seen in most bacteria and plants, the other is the Kaminoadipate (AAA) pathway from 2-oxoglutarate via AAA, as seen in yeast [1] and fungi [2,3]. In our recent studies, however, an extremely thermophilic bacterium, Thermus thermophilus HB27, was shown to synthesize lysine not via DAP, but through AAA [4].…”