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.
The evolutionary history of tree constructed from nucleotide sequences of the 16S rDNA gene was inferred using the Neighbor-Joining method . The bootstrap consensus tree inferred from replicates is taken to represent the evolutionary history of the taxa analyzed . The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test replicates are shown next to the branches . The evolutionary distances were computed using the Maximum Composite Likelihood method  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 positions in the final dataset. On the other hand, The evolutionary distances for amino acid based tree were computed using the Poisson correction method  and are in the units of the number of amino acid substitutions per site. The analysis involved 52 amino acid sequences. 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. Dabbagh, F. Phylogeny of urate oxidase producing bacteria: on the basis of gene sequences of 16S rRNA and uricase protein. Iranian Journal of Pharmaceutical Sciences , 8 2 , Iranian Journal of Pharmaceutical Sciences , 8, 2, , Iranian Journal of Pharmaceutical Sciences , ; 8 2 : Toggle navigation.
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 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. Full Text. Table 1. Uricase producing bacteria included in this study.
A new metal-chelated beads for reversible use in uricase adsorption. J Mol Catal B: Enzym ; Human urate oxidase gene: cloning and partial sequence analysis reveal a stop codon within the fifth exon. Biochem Biophys Res Commun ; Therapeutic proteins: a comparison of chemical and biological properties of uricase conjugated to linear or branched poly ethylene glycol and poly N-acryloylmorpholine. Farmaco ; J Biosci Bioeng ; Transthyretin-related proteins function to facilitate the hydrolysis of 5-hydroxyisourate, the end product of the uricase reaction.
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Physiology, phylogeny, and LUCA
Forgot password? Old Password. What is the point of calling the terminal taxa in prokaryotic phylogenies "species", beyond a wholly spurious analogy with eukaryotes? None of the definitions of "species" that are generally applied to eukaryotes can be applied to prokaryotes for the simple reason that the latter do not couple reproduction with sexual recombination. The Dobzhansky-Mayr "biological species concept" is like Darwin's based on reproductive isolation; to be members of the same species, two individuals must be capable of interbreeding and producing fertile offspring under "natural" conditions.
Prokaryotes simply don't do this at all. Speciation is a property only of nucleated organisms. There is no problem of "species" in evolutionary biology. Which isn't obviously always possible because Nature is more complex than we wish it to be.
ANY classification is oversimplification of reality. And so yes, taxonomy in prokaryotes is much more difficult but is not fundamentally different from eukaryotes.
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We still need to call different bacteria different names, right? So why not "species"? If species don't exist in procaryotes then what does exist?
But it's just a word. You could also check out this recent paper on defining species in strictly asexual rotifers for a way to treat speciation where recombination and reproduction have been decoupled. Allen MacNeill, What is the point of calling the terminal taxa in prokaryotic phylogenies "species", beyond a wholly spurious analogy with eukaryotes?
You have to call them something and "species" is as good as anything on a blog such as this. I'm well aware of the problems with defining "species.
Perhaps you could share it with us? BTW, this part of your comment is dead wrong. How, precisely, is the statement "dead wrong"? Seems to me there are several possibilities: 1 That's not what Darwin, Dobzhansky, and Mayr said 2 The "biological species concept" isn't based on reproductive isolation 3 Reproduction in prokaryotes is indeed coupled with sexual recombination in essentially the same way it is in eukaryotes especially animals 4 Prokaryotes can be "fertile" or "infertile" in the same way that eukaryotes can I'm curious; which of these assertions do you agree with, and on what evidence?
The reason I don't like to use the term "species" to refer to the termini of prokaryote phylogenies is that it conveys all the wrong ideas about what phylogenies are all about. Focusing on reproductive incompatibility has little or no bearing on diversification among prokaryotes, and is hopelessly muddled by the problem of horizontal gene transfer.
Indeed, I would go further: I think the whole idea of "species" is a holdover from Platonic typological thinking, and has done little or nothing to advance our understanding of how genetic and phenotypic diversification has proceeded in most phylogenies, including animals the only group in which reproductive incompatibility plays a crucial role in phylogenetic diversification. Allen MacNeill said: "Species", in other words, are a figment of the human imagination. And so are colors.
Materials and Methods
The whole idea of color "green" is a holdover from Platonic typological thinking and has done little or nothing to advance our understanding of how electromagnetic waves are perceived by photoreceptors. Strangely enough, I still find it useful. Allen MacNeill asks, How, precisely, is the statement "dead wrong"? Seems to me there are several possibilities This part is dead wrong. Many bacteria "species" have something akin to sex where individuals can exchange alleles,.
Well 1 thanks for writing about our paper I just want to chime in on the species issue. I think there is no reason why we cannot use the term species for bacterial groups. To me, that is good enough to call things a species as it indicates some higher rate of gene flow within the group than between. Sure, lateral transfer messes things up, but it seems to not have eliminated consistent groupings whether you believe Ford Doolittles argument about what this means or not.
It's wonderful for a layperson like me to be able to read about research like this.
Physiology and Molecular Phylogeny of Bacteria Isolated from Alkaline Distillery Lime – PJM ONLINE
I've looked at the figure reproduced in the post in the PDF version at Genome Biology, at a high enough zoom level for my middle-aged eyes to read text. What I see there leads me to the following question: Do the results tend to show bacteria such as Thermus thermophilus and Deinococcus geothermalis at the base of the phylogenetic tree?
If so, this may be something well-understood in the field, but I hadn't known it and find it interesting.
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