Gene Context Analysis Reveals Functional Divergence between Hypothetically Equivalent Enzymes of the Purine–Ureide Pathway

Abstract

A major problem of genome annotation is the assignment of a function to a large number of genes of known sequences through comparison with a relatively small number of experimentally characterized genes. Because functional divergence is a widespread phenomenon in gene evolution, the transfer of a function to homologous genes is not a trivial exercise. Here, we show that a family of homologous genes which are found in purine catabolism clusters and have hypothetically equivalent functions can be divided into two distinct groups based on the genomic distribution of functionally related genes. One group (UGLYAH) encodes proteins that are able to release ammonia from (S)-ureidoglycine, the enzymatic product of allantoate amidohydrolase (AAH), but are unable to degrade allantoate. The presence of a gene encoding UGLYAH implies the presence of AAH in the same genome. The other group (UGLYAH2) encodes proteins that are able to release ammonia from (S)-ureidoglycine as well as urea from allantoate. The presence of a gene encoding UGLYAH2 implies the absence of AAH in the same genome. Because (S)-ureidoglycine is an unstable compound that is only formed by the AAH reaction, the in vivo function of this group of enzymes must be the release of urea from allantoate (allantoicase activity), while ammonia release from (S)-ureidoglycine is an accessory activity that evolved as a specialized function in a group of genes in which the coexistence with AAH was established. Insights on the active site modifications leading to a change in the enzyme activity were provided by comparison of three-dimensional structures of proteins belonging to the two different groups and by site-directed mutagenesis. Our results indicate that when the neighborhood of uncharacterized genes suggests a role in the same process or pathway of a characterized homologue, a detailed analysis of the gene context is required for the transfer of functional annotations.

The ropAe gene encodes a porin‐like protein involved in copper transit in Rhizobium etli CFN42

“…Furthermore, the location of the four ropA homologs in different gene contex (Table S7) suggests that these genes could be following different evolutionary pathways, as has been observed in genes from other models analyzed with different bioinformatic gene contex tools (Dewey, ; Martinez‐Guerrero, Ciria, Abreu‐Goodger, Moreno‐Hagelsieb, & Merino, ; Puggioni et al., ; Seret & Baret, ). In support of the functional divergence hypothesis and outer membrane protein localization, it was recently reported that two R. etli RopAe paralogs, RopAch1 and RopAch2, were found to be expressed in the exoproteome of this organism when exposed to the plant flavonoid naringenin (Meneses et al., ).…”

Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions

“…Gene AKAUv1_1780022 is predicted to encode an allantoicase with a potential role in the transformation of purines or the nitrogen-rich derivative allantoin [46], releasing nitrogen for anabolism [47, 48]. Moreover, the upregulated gene AKAUv1_3070011, that was predicted to encode 3-hydroxy isobutyrate dehydrogenase, might be involved in the valine/leucine degradation pathway (Table S7).…”

The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme

“…There is no information about urate utilization by A. fabrum , although the presence of a COG3748 gene (Atu2314, verified by sequencing of our laboratory strain), urah and urad genes (see Fig. 1c ), as well as other downstream genes of the catabolic pathway 32 , suggest that A. fabrum is able to use urate as a nitrogen source. While in animals purine degradation is used to eliminate excess nitrogen, in plant, fungi, and prokaryotes this pathway is important for the recovery of mineral nitrogen from endogenous or imported purines 33 34 .…”