Abstract
BackgroundUrea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms.ResultsAmong the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina.ConclusionsWe conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay.
Highlights
Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process
In Navarathna et al [1], we suggested that urea amidolyase likely arose before the divergence of the hemiascomycetes and the euascomycetes, c. 350 - 400 million years ago, by insertion of a gene encoding allophanate hydrolase into a methylcrotonyl CoA carboxylase gene, creating DUR1,2 and inactivating mccA
We studied the distribution of urea amidolyase, urea carboxylase, and urease proteins in various species across all kingdoms, and biotin-carboxylation domain containing proteins, i.e., Acc1, pyruvate carboxylase (Pyc), propionyl-CoA carboxylase (PccA), and methylcrotonoyl-CoA carboxylase (MccA), in various fungal species
Summary
Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes It contains two major domains: the amidase and urea carboxylase domains. Urea amidolyase is an energy dependent biotin-containing enzyme It is encoded by the DUR1,2 gene and was first characterized in the yeast Candida utilis, known as Pichia jadinii [3]. Urease and urea amidolyase activities were not observed together in the same green algal species; it was either one or the other [4,5] This cytoplasmic, biotin-dependent enzyme [6] consists of a single polypeptide chain with regions for urea carboxylase (EC 6.3.4.6) and allophanate hydrolase ( known as amidase; EC 3.5.1.54) activity. Two adjacent genes (DUR1 and DUR2) were originally considered to encode the two enzymes; but later they were renamed as a single gene, DUR1,2 [7]
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