Gene acquisition, duplication and metabolic specification: the evolution of fungal methylisocitrate lyases

Abstract

Gene duplication represents an evolutionary mechanism for expanding metabolic potential. Here we analysed the evolutionary relatedness of isocitrate and methylisocitrate lyases, which are key enzymes of the glyoxylate and methylcitrate cycle respectively. Phylogenetic analyses imply that ancient eukaryotes acquired an isocitrate lyase gene from a prokaryotic source, but it was lost in some eukaryotic lineages. However, protists, oomycetes and most fungi maintained this gene and successfully integrated the corresponding enzyme into the glyoxylate cycle. A second gene, encoding a highly related enzyme, is present in fungi, but absent from other eukaryotes. This methylisocitrate lyase is specifically involved in propionyl-CoA degradation via the methylcitrate cycle. Although bacteria possess methylisocitrate lyases with a structural fold similar to that of isocitrate lyases, their sequence identity to fungal methylisocitrate lyases is low. Phylogenetic analyses imply that fungal methylisocitrate lyases arose from gene duplication of an ancient isocitrate lyase gene from the basidiomycete lineage. Mutagenesis of active-site residues of a bacterial and fungal isocitrate lyase, which have been predicted to direct the substrate specificity of iso- and methylisocitrate lyases, experimentally confirmed the possibility of direct evolution of methylisocitrate lyases from isocitrate lyases. Thus, gene duplication has increased the metabolic capacity of fungi.

Candida albicans Utilizes a Modified β-Oxidation Pathway for the Degradation of Toxic Propionyl-CoA

“…Analysis revealed the sole presence of the putative citrate synthase Cit1p (orf19.4393), but no additional methylcitrate synthase. To check for a specific methylisocitrate lyase, Icl2p from S. cerevisiae (30) and MclA from A. fumigatus (25) were used as templates, but they only revealed the phylogenetically closely related isocitrate lyase Icl1p (orf19.6844) from C. albicans (4,11,25). When the putative methylcitrate dehydratase from S. cerevisiae (accession number NP_015326) or A. fumigatus (accession number EDP47611) was used for BLASTP analyses, no homologue was detected in the C. albicans genome.…”

“…The methyl citrate cycle is common in Ascomycota such as Aspergillus species (19,20), Fusarium species (57,58), and the yeast S. cerevisiae (30,46). Furthermore, genes encoding enzymes of the methyl citrate cycle have also been detected in Basidiomycota (25), which led to the assumption that this pathway is the general mechanism by which fungi degrade propionyl-CoA. However, exceptions for use of a modified ␤-oxidation pathway had been proposed for C. rugosa and Candida catenulata (34).…”

“…In contrast, most fungi seem to use the so-called methyl citrate cycle for the degradation of propionyl-CoA (24). This pathway, which is also present in several bacteria (25), results in the ␣-oxidation of propionate to pyruvate and is characterized by an initial condensation of propionyl-CoA and oxaloacetate to form methyl citrate (19), a dehydration to methylcis-aconitate (26), a rehydration to methyl isocitrate (26), and finally, a cleavage via methylisocitrate lyase into pyruvate and succinate (27)(28)(29)(30). Although the reactions of this pathway resemble those of the citric acid and the glyoxylate cycle, the methyl citrate cycle uses its own specific set of enzymes.…”

Phylogenetic and phenotypic characterisation of the 3-ketoacyl-CoA thiolase gene family from the opportunistic human pathogenic fungusCandida albicans

“…However, Fox3p might only have a supportive function because POT1 was essential on all fatty acids tested. Nevertheless, gene duplication and subsequent specification of the resulting duplicates for a specific environmental condition or to encounter new substrates for metabolism appear common among fungi (M€ uller et al, 2011;Fazius et al, 2012), and FOX3 adds another example for such a process.…”

The fungal α‐aminoadipate pathway for lysine biosynthesis requires two enzymes of the aconitase family for the isomerization of homocitrate to homoisocitrate

“…The phylogenetic relationship between Aco1p and Aco2p implies that one enzyme derived from a gene duplication event with subsequent specification for the new substrate and metabolic pathway. This process is similar to the evolution of fungal methylisocitrate lyases from isocitrate lyases and seems to depict a general mechanism in fungi to enhance and adapt their metabolic potential (Müller et al ., ).…”