Phylogeny of urate oxidase producing bacteria: on the basis of gene sequences of 16S rRNA and uricase protein

Document Type: Research Paper

Authors

Department of Pharmaceutical Biotechnology, Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran

Abstract

      Uricase or Urate oxidase (urate:oxygen oxidoreductase, EC 1.7.3.3), a peroxisomal enzyme which is found in many bacteria, catalyzes the oxidative opening of the purine ring of urate to yield allantoin, carbon dioxide, and hydrogen peroxide. In this study, the phylogeny of urate oxidase (uricase) producing bacteria was studied based on gene sequences of 16S rRNA and uricase protein. Representative and type strains (52 strains total) of most of the known species were analyzed. The acquired sequences (rDNA sequences of the 16S rRNA genes and the amino acid sequences of uricase) were aligned with the Clustal W program using MEGA software version 4.0. Phylogenetic trees were constructed with the neighbor-joining method, and were bootstrapped with 500 replications of each sequence. The large congruence of phylogenetic relationship between the uricase gene and of 16S rRNA gives considerable support to the phylogeny of urate oxidase producing bacteria which was previously suggested on the basis of 16S rRNA sequences. The observed consistency promotes the idea that each of these genes shared a common evolutionary history in uricase producing bacteria we have analyzed.

Keywords


1.Introduction  

     Uricase or Urate oxidase (urate:oxygen oxidoreductase, EC 1.7.3.3), a peroxisomal enzyme, catalyzes the oxidative opening of the purine ring of urate to yield allantoin, carbon dioxide, and hydrogen peroxide [1-2]. The enzyme is a tetramer, consisting of two types of different subunits with a final molecular weight ranging from 145 to 150 kDa [3]. A number of bacteria are able to produce uricase, including, but not limited to, Pseudomonas aeruginosa, Arthrobacter globiformis, Bacillus subtilis, Bacillus fastidious, Nocardia farcinica and Microbacterium sp. [4-12]. This enzyme has also been reported in fungi, plants and animals [13-15]. It has a unique evolutionary feature, in that the enzyme has been lost during primate evolution with no obvious explanation [16]. The biological reason for the loss of urate oxidase activity in humans and certain primates is unknown. According to one view, this loss has had a distinctly beneficial effect.

     It has been shown that uric acid is a powerful antioxidant and a scavenger of free radicals; therefore, a high serum uric acid level caused by the loss of urate oxidase activity may have contributed to a decreased cancer rate and a lengthened hominoid life span [17]. In order to investigate the genetic relationships among the uricase producing bacteria further, sequences of another gene not related to the 16S rRNA should be considered. Therefore, in this report, we compare the genetic relationships of the uricase producing bacteria based on 16S rDNA sequences and on uricase amino acid sequences.

 

2. Material and Methods

 Data Collection

      Here, representative and type strains (52 strains total) of most of the known bacterial species were analyzed. Almost all 16S rDNA sequences and uricase amino acid sequences were collected from the National Center for Biotechnology Information (http:// www.ncbi.nlm.nih.gov). List of all these 52 strains and the GenBank accession numbers for genomes used in this study are listed in Table 1.

 Phylogenetic analysis 

    The acquired sequences (rDNA sequences of the 16S rRNA genes and the amino acid sequences of uricase) were aligned with the Clustal W program using MEGA software version 4.0 [18]. Phylogenetic trees were constructed with the neighbor-joining method, and were bootstrapped with 500 replications of each sequence.

Figure 1. Neighbor-joining tree constructed from amino acid sequences of the uricase showing the phylogenetic relationships. Bootstrap values above 50 are indicated at the main nodes. Bootstrap values are given above branches.


Figure 2. Neighbor-joining tree constructed from nucleotide sequences of the 16S rDNA gene showing the phylogenetic relationships. Bootstrap values above 50 are indicated at the main nodes. Bootstrap values are given above branches.

Table 1. Uricase producing bacteria included in this study.

Species

Strain

GenBank Accession number

Acidobacterium sp.

MP5ACTX8

NZ_ADVX01000009.1

Actinosynnema mirum

DSM 43827

NC_013093.1

Arthrobacter aurescens

TC1

NC_008711.1

Arthrobacter chlorophenolicus

A6

NC_011886.1

Bacillus clausii

KSM-K16

NC_006582.1

Bacillus halodurans

C-125

NC_002570.2

Bacillus selenitireducens

MLS10

NC_014219.1

Bacillus subtilis

str. 168

NZ_ABQK01000005.1

Bacillus tusciae

DSM 2912

CP002017.1

Brachybacterium faecium

DSM 4810

NC_013172.1

Burkholderia cenocepacia

J2315

NC_011000.1

Burkholderia pseudomallei

K96243

NC_006350.1

Catenulispora acidiphila

DSM 44928

NC_013131.1

Cellulomonas flavigena

DSM 20109

CP001964.1

Chitinophaga pinensis

DSM 2588

NC_013132.1

Comamonas testosteroni

CNB-2

NC_013446.1

Deinococcus radiodurans

R1

NC_001263.1

Dickeya dadantii

3937

NC_014500.1

Erwinia amylovora

CFBP1430

NC_013961.1

Erwinia pyrifoliae

DSM 12163

FN392235.1

Frankia alni

ACN14a

NC_008278.1

Geodermatophilus obscures

DSM 43160

NC_013757.1

Kineococcus radiotolerans

SRS30216

NC_009664.2

Kocuria rhizophila

DC2201

AP009152.1

Ktedonobacter racemifer

DSM 44963

ADVG01000003.1

Methylobacterium nodulans

ORS 2060

NC_011894.1

Methylobacterium radiotolerans

JCM 2831

NC_010505.1

Mycobacterium smegmatis

MC2 155

NC_008596.1

Nakamurella multipartite

DSM 44233

NC_013235.1

Nocardia farcinica

IFM 10152

NC_006361.1

Nocardiopsis dassonvillei

DSM 43111

CP002040.1

Paenibacillus sp.

JDR-2

NC_012914.1

Pantoea vagans

C9-1

NC_014562.1

Pseudomonas aeruginosa

PAO1

NC_002516.2

Pseudomonas fluorescens

SBW25

NC_012660.1

Ralstonia eutropha

JMP134

NC_007347.1

Rhizobium leguminosarum

bv. viciae 3841

NC_008380.1

Rhodococcus erythropolis

PR4

NC_012490.1

Rhodococcus opacus

B4

AP011115.1

Rubrobacter xylanophilus

DSM 9941

NC_008148.1

Saccharopolyspora erythraea

NRRL2338

AM420293.1

Solibacter usitatus

Ellin6076

CP000473.1

Sorangium cellulosum

So ce 56

NC_010162.1

Stackebrandtia nassauensis

DSM 44728

CP001778.1

Starkeya novella

DSM 44728

CP002026.1

Streptomyces avermitilis

DSM 506

BA000030.3

Streptomyces bingchenggensis

MA-4680

CP002047.1

Streptomyces griseus

NBRC 13350

AP009493.1

Streptomyces scabiei

87.22

FN554889.1

Streptosporangium roseum

DSM 43021

NC_013595.1

Thermobispora bispora

DSM 43833

CP001874.1

Truepera radiovictrix

DSM 17093

CP002049.1

3. Results

 Phylogeny according to 16S rDNA sequences and uricase amino acid sequences

    The phylogenetic tree based on uricase amino acid sequences (Figure 1) revealed a tree topology which was generally similar to the 16S rDNA tree (Figure 2). The large congruence of phylogenetic relationship between the uricase gene and of 16S rDNA gives considerable support to the phylogeny of urate oxidase producing bacteria previously suggested on the basis of 16S rDNA sequences. The similar position of

 Strepomyces, Bacillus, Arthrobacter and Erwinia species indicate that the phylogenetic tree based on uricase amino acid sequences (Figure 1) was highly consistent with the 16S rDNA tree (Figure 2), suggesting that each of these genes shared a common evolutionary history in uricase producing bacteria we have analyzed in this study.

 

4. Discussion

      The evolutionary history of tree constructed from nucleotide sequences of the 16S rDNA gene was inferred using the Neighbor-Joining method [19]. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed [20]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [20]. The evolutionary distances were computed using the Maximum Composite Likelihood method [21] and are in the units of the number of base substitutions per site. The analysis involved 52 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 971 positions in the final dataset. On the other hand, The evolutionary distances for amino acid based tree were computed using the Poisson correction method [22] and are in the units of the number of amino acid substitutions per site. The analysis involved 52 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 142 positions in the final dataset.

      The infrageneric groups retained in 16S rDNA nucleotide analysis only partly reflect the current taxonomical classification of these bacteria. It should be kept in mind that a more complete sample of urate oxidase species will considerably enhance the phylogenetic resolution and closely reflects the results of analysis.

      The uricase-producing bacteria represent a phylogenetically coherent group of bacteria, which are also closely related according to the 16S rDNA sequence. By comparison of the sequences of both genes, an improved relationship for the uricase-producing bacteria could be established. This observation is quite remarkable and strongly supports the 16S-rDNA-based phylogeny of these bacteria. High bootstrap values at most of the branching points suggest that the analysis has a high degree of reliability. However, more detailed studies including a higher number of accessions are necessary to test this hypothesis.



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