Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes

Abstract

The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH , purP , purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ , respectively. In Bacteria , these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea , these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea . Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. Based on the results, we propose that the gene purO was present in the common ancestor of all living beings, whereas the gene encoding PurP emerged after the divergence of Archaea and Bacteria and their isoforms originated in duplication events in the common ancestor of phyla Crenarchaeota and Euryarchaeota . The results reported here expand our understanding of the diversity and evolution of the last two steps of the purine biosynthetic pathway in prokaryotes.

Experimental characterization of two archaeal inosine 5'-monophosphate cyclohydrolases

“…In Archaea, the enzymes involved are more diverse, with a patchy distribution of two unrelated IMP cyclohydrolases (PurO and PurH2) and two AICAR formyltransferases (10-formyltetrahydrofolate-requiring PurH1 and folate-independent PurP). There is little correlation between the presence of genes encoding 10-formyltetrahydrofolate-requiring PurH1 or formate-requiring PurP and the presence of genes encoding PurO or PurH2, with all four possible patterns occurring in archaea, as previously described [1, 2] and shown in Fig 1. In this paper, we report the kinetic characterization of two selected archaeal IMP cyclohydrolases, one each of the PurO and PurH2 types, to increase the diversity of experimentally-characterized IMP cyclohydrolases within the archaeal domain.…”

“…While this predicted protein has the residues determined to be important for binding and catalysis in the two PurOs characterized in methanogens [3], overall amino acid identity between Thermococcus kodakarensis PurO and previously-characterized PurOs is only 32–35%. The genomes of closely-related Pyrococci have no evidence for an IMP cyclohydrolase of either the PurO or PurH2 type, despite an otherwise complete predicted pathway, implying the existence of a third IMP cyclohydrolase enzyme, previously posited [1, 2, 7]. Thus, given this confusing genomic context modest sequence identity to experimentally-characterized PurOs, the predicted PurO from T .…”

“…Based on the limited sequence data available at the time, PurO was originally described as an archaeal signature protein [5], but it is uniformly absent from the Crenarchaeaota and Thaumarchaeota. It might be described as a Euryarchaeal signature protein (although present in only 34 of 95 sequenced Euryarchaea [2]), except that genes encoding proteins similar to PurO are also reported in a tiny fraction of sequenced bacteria (22 of 1266 [2]).…”

Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

“…2H and S12; Lindell et al ., 2004; Sullivan et al ., 2006; Ignacio‐Espinoza and Sullivan, 2012). However, in the case of purH , this interlacing pattern is a result of the host gene, a bifunctional two domain protein that carries out two sequential steps of the purine biosynthesis pathway (Zhang et al ., 2008), split into two distinct genes, better named purV and purJ (Costa Brandão Cruz et al ., 2019), each with a single functional domain (Supporting Information Fig. S13B).…”