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Molecular evolution of adenylating domain of aminoadipate reductase.

An KD, Nishida H, Miura Y, Yokota A - BMC Evol. Biol. (2003)

Bottom Line: Aminoadipate reductase (Lys2) is a fungal-specific protein.A similar primary structure can be found in some bacterial antibiotic/peptide synthetases.Phylogenetic trees revealed that the lys2 genes are monophyletic; on the other hand, bacterial antibiotic/peptide synthase genes were not found to be monophyletic.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan. aa17122@mail.ecc.u-tokyo.ac.jp

ABSTRACT

Background: Aminoadipate reductase (Lys2) is a fungal-specific protein. This enzyme contains an adenylating domain. A similar primary structure can be found in some bacterial antibiotic/peptide synthetases. In this study, we aimed to determine which bacterial adenylating domain is most closely related to Lys2. In addition, we analyzed the substitution rate of the adenylating domain-encoding region.

Results: Some bacterial proteins contain more than two similar sequences to that of the adenylating domain of Lys2. We compared 67 amino acid sequences from 37 bacterial and 10 fungal proteins. Phylogenetic trees revealed that the lys2 genes are monophyletic; on the other hand, bacterial antibiotic/peptide synthase genes were not found to be monophyletic. Comparative phylogenetic studies among closely related fungal lys2 genes showed that the rate of insertion/deletion in these genes was lower and the nucleotide substitution rate was higher than that in the internal transcribed spacer (ITS) regions.

Conclusions: The lys2 gene is one of the most useful tools for revealing the phylogenetic relationships among fungi, due to its low insertion/deletion rate and its high substitution rate. Lys2 is most closely related to certain bacterial antibiotic/peptide synthetases, but a common ancestor of Lys2 and these synthetases evolutionarily branched off in the distant past.

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Alignment of the selected 27 amino acid sequences. This alignment was used in the maximum likelihood analysis. Protein names were shown in Materials and Methods.
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Figure 2: Alignment of the selected 27 amino acid sequences. This alignment was used in the maximum likelihood analysis. Protein names were shown in Materials and Methods.

Mentions: In order to determine which bacterial domain was most closely related to that of Lys2, a maximum likelihood analysis using PHYLIP version 3.6 [14] was carried out. We selected 27 amino acid sequences from the 67 sequences used in the neighbor-joining analysis. The alignment used in maximum likelihood analysis is shown in Fig. 2. The phylogenetic tree (Fig. 3) indicates that a protein (AGR L 2311) from Agrobacterium tumefaciens is most closely related to a common ancestor of Lys2, but this result had only weak bootstrap support (17%). In the bootstrap consensus tree (Fig. 3), the branch points at the early stage of evolution are very weak support. Animals and plants have no Lys2. If the common ancestor of eukaryotes had a similar protein, the other eukaryotes except for fungi had lost it.


Molecular evolution of adenylating domain of aminoadipate reductase.

An KD, Nishida H, Miura Y, Yokota A - BMC Evol. Biol. (2003)

Alignment of the selected 27 amino acid sequences. This alignment was used in the maximum likelihood analysis. Protein names were shown in Materials and Methods.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC156885&req=5

Figure 2: Alignment of the selected 27 amino acid sequences. This alignment was used in the maximum likelihood analysis. Protein names were shown in Materials and Methods.
Mentions: In order to determine which bacterial domain was most closely related to that of Lys2, a maximum likelihood analysis using PHYLIP version 3.6 [14] was carried out. We selected 27 amino acid sequences from the 67 sequences used in the neighbor-joining analysis. The alignment used in maximum likelihood analysis is shown in Fig. 2. The phylogenetic tree (Fig. 3) indicates that a protein (AGR L 2311) from Agrobacterium tumefaciens is most closely related to a common ancestor of Lys2, but this result had only weak bootstrap support (17%). In the bootstrap consensus tree (Fig. 3), the branch points at the early stage of evolution are very weak support. Animals and plants have no Lys2. If the common ancestor of eukaryotes had a similar protein, the other eukaryotes except for fungi had lost it.

Bottom Line: Aminoadipate reductase (Lys2) is a fungal-specific protein.A similar primary structure can be found in some bacterial antibiotic/peptide synthetases.Phylogenetic trees revealed that the lys2 genes are monophyletic; on the other hand, bacterial antibiotic/peptide synthase genes were not found to be monophyletic.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan. aa17122@mail.ecc.u-tokyo.ac.jp

ABSTRACT

Background: Aminoadipate reductase (Lys2) is a fungal-specific protein. This enzyme contains an adenylating domain. A similar primary structure can be found in some bacterial antibiotic/peptide synthetases. In this study, we aimed to determine which bacterial adenylating domain is most closely related to Lys2. In addition, we analyzed the substitution rate of the adenylating domain-encoding region.

Results: Some bacterial proteins contain more than two similar sequences to that of the adenylating domain of Lys2. We compared 67 amino acid sequences from 37 bacterial and 10 fungal proteins. Phylogenetic trees revealed that the lys2 genes are monophyletic; on the other hand, bacterial antibiotic/peptide synthase genes were not found to be monophyletic. Comparative phylogenetic studies among closely related fungal lys2 genes showed that the rate of insertion/deletion in these genes was lower and the nucleotide substitution rate was higher than that in the internal transcribed spacer (ITS) regions.

Conclusions: The lys2 gene is one of the most useful tools for revealing the phylogenetic relationships among fungi, due to its low insertion/deletion rate and its high substitution rate. Lys2 is most closely related to certain bacterial antibiotic/peptide synthetases, but a common ancestor of Lys2 and these synthetases evolutionarily branched off in the distant past.

Show MeSH
Related in: MedlinePlus