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

Doniselli N, Monzeglio E, Dal Palù A, Merli A, Percudani R - Sci Rep (2015)

Bottom Line: In contrast with the known soluble Uox, the identified gene (puuD) encodes a membrane protein with a C-terminal cytochrome c.The 8-helix transmembrane domain corresponds to DUF989, a family without similarity to known proteins.These findings identify a missing link in purine catabolism, assign a biochemical activity to a domain of unknown function (DUF989), and complete the catalytic repertoire of an enzyme useful for human therapy.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Parma, Italy.

ABSTRACT
In living organisms, the conversion of urate into allantoin requires three consecutive enzymes. The pathway was lost in hominid, predisposing humans to hyperuricemia and gout. Among other species, the genomic distribution of the two last enzymes of the pathway is wider than that of urate oxidase (Uox), suggesting the presence of unknown genes encoding Uox. Here we combine gene network analysis with association rule learning to identify the missing urate oxidase. In contrast with the known soluble Uox, the identified gene (puuD) encodes a membrane protein with a C-terminal cytochrome c. The 8-helix transmembrane domain corresponds to DUF989, a family without similarity to known proteins. Gene deletion in a PuuD-encoding organism (Agrobacterium fabrum) abolished urate degradation capacity; the phenotype was fully restored by complementation with a cytosolic Uox from zebrafish. Consistent with H2O2 production by zfUox, urate oxidation in the complemented strain caused a four-fold increase of catalase. No increase was observed in the wild-type, suggesting that urate oxidation by PuuD proceeds through cytochrome c-mediated electron transfer. These findings identify a missing link in purine catabolism, assign a biochemical activity to a domain of unknown function (DUF989), and complete the catalytic repertoire of an enzyme useful for human therapy.

No MeSH data available.


Related in: MedlinePlus

Distribution of urate oxidation genes in monoderm and diderm prokaryotes.The occurrence of the different genes for urate oxidation in 341 prokaryotic species (see Fig. 1c) classified based on the presence of a single (monoderm) or a double (diderm) cell membrane40.
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f5: Distribution of urate oxidation genes in monoderm and diderm prokaryotes.The occurrence of the different genes for urate oxidation in 341 prokaryotic species (see Fig. 1c) classified based on the presence of a single (monoderm) or a double (diderm) cell membrane40.

Mentions: We have described the identification of a protein family of unknown function (COG3478) as an integral membrane, cytochrome c urate oxidase (PuuD). This identification was initially suggested by the analysis of the gene association network (Fig. 1b) and then confirmed by the analysis of gene distribution (Fig. 1c), as quantitatively evaluated through the use of association rules (Table 1). This method, inspired by the logic extension28 of the widely used correlated and anti-correlated phylogenetic profiles2627, can be useful in the presence of functional associations not adequately described by pairwise relations, as exemplified here. The same analysis that enabled the functional assignment of COG3748, also provides evidence that the identification of PuuD completes the genetic repertoire of enzymes involved in urate oxidation. There is a very small number of cases in which any of the four urate oxidation genes is found in the absence of urah and urad, suggesting that there are no alternative genes encoding these enzymatic activities; on the other hand, among the 1689 different species considered there are only twelve cases in which the presence of urah and urad is not explained by the presence of uox, hpxO, hpyO, or puuD genes (Table 1). Most of these exceptions can be explained by errors of the gene identification procedure (Supplementary Table S1). Genes encoding PuuD urate oxidase have a peculiar organism distribution, being found only in aerobic bacteria with two cell membranes -diderms, approximately corresponding to gram-negative in the traditional classification40. In these organisms, PuuD is the prevalent form of urate oxidase, while Uox is prevalent in monoderm (~gram-positive) prokaryotes (Fig. 5).


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

Doniselli N, Monzeglio E, Dal Palù A, Merli A, Percudani R - Sci Rep (2015)

Distribution of urate oxidation genes in monoderm and diderm prokaryotes.The occurrence of the different genes for urate oxidation in 341 prokaryotic species (see Fig. 1c) classified based on the presence of a single (monoderm) or a double (diderm) cell membrane40.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4562309&req=5

f5: Distribution of urate oxidation genes in monoderm and diderm prokaryotes.The occurrence of the different genes for urate oxidation in 341 prokaryotic species (see Fig. 1c) classified based on the presence of a single (monoderm) or a double (diderm) cell membrane40.
Mentions: We have described the identification of a protein family of unknown function (COG3478) as an integral membrane, cytochrome c urate oxidase (PuuD). This identification was initially suggested by the analysis of the gene association network (Fig. 1b) and then confirmed by the analysis of gene distribution (Fig. 1c), as quantitatively evaluated through the use of association rules (Table 1). This method, inspired by the logic extension28 of the widely used correlated and anti-correlated phylogenetic profiles2627, can be useful in the presence of functional associations not adequately described by pairwise relations, as exemplified here. The same analysis that enabled the functional assignment of COG3748, also provides evidence that the identification of PuuD completes the genetic repertoire of enzymes involved in urate oxidation. There is a very small number of cases in which any of the four urate oxidation genes is found in the absence of urah and urad, suggesting that there are no alternative genes encoding these enzymatic activities; on the other hand, among the 1689 different species considered there are only twelve cases in which the presence of urah and urad is not explained by the presence of uox, hpxO, hpyO, or puuD genes (Table 1). Most of these exceptions can be explained by errors of the gene identification procedure (Supplementary Table S1). Genes encoding PuuD urate oxidase have a peculiar organism distribution, being found only in aerobic bacteria with two cell membranes -diderms, approximately corresponding to gram-negative in the traditional classification40. In these organisms, PuuD is the prevalent form of urate oxidase, while Uox is prevalent in monoderm (~gram-positive) prokaryotes (Fig. 5).

Bottom Line: In contrast with the known soluble Uox, the identified gene (puuD) encodes a membrane protein with a C-terminal cytochrome c.The 8-helix transmembrane domain corresponds to DUF989, a family without similarity to known proteins.These findings identify a missing link in purine catabolism, assign a biochemical activity to a domain of unknown function (DUF989), and complete the catalytic repertoire of an enzyme useful for human therapy.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Parma, Italy.

ABSTRACT
In living organisms, the conversion of urate into allantoin requires three consecutive enzymes. The pathway was lost in hominid, predisposing humans to hyperuricemia and gout. Among other species, the genomic distribution of the two last enzymes of the pathway is wider than that of urate oxidase (Uox), suggesting the presence of unknown genes encoding Uox. Here we combine gene network analysis with association rule learning to identify the missing urate oxidase. In contrast with the known soluble Uox, the identified gene (puuD) encodes a membrane protein with a C-terminal cytochrome c. The 8-helix transmembrane domain corresponds to DUF989, a family without similarity to known proteins. Gene deletion in a PuuD-encoding organism (Agrobacterium fabrum) abolished urate degradation capacity; the phenotype was fully restored by complementation with a cytosolic Uox from zebrafish. Consistent with H2O2 production by zfUox, urate oxidation in the complemented strain caused a four-fold increase of catalase. No increase was observed in the wild-type, suggesting that urate oxidation by PuuD proceeds through cytochrome c-mediated electron transfer. These findings identify a missing link in purine catabolism, assign a biochemical activity to a domain of unknown function (DUF989), and complete the catalytic repertoire of an enzyme useful for human therapy.

No MeSH data available.


Related in: MedlinePlus