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Turning points in the evolution of peroxidase-catalase superfamily: molecular phylogeny of hybrid heme peroxidases.

Zámocký M, Gasselhuber B, Furtmüller PG, Obinger C - Cell. Mol. Life Sci. (2014)

Bottom Line: In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain.Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily.We present and discuss their phylogeny, sequence signatures and putative biological function.

View Article: PubMed Central - PubMed

Affiliation: Division of Biochemistry, Department of Chemistry, VIBT, Vienna Institute of BioTechnology, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria, marcel.zamocky@boku.ac.at.

ABSTRACT
Heme peroxidases and catalases are key enzymes of hydrogen peroxide metabolism and signaling. Here, the reconstruction of the molecular evolution of the peroxidase-catalase superfamily (annotated in pfam as PF00141) based on experimentally verified as well as numerous newly available genomic sequences is presented. The robust phylogenetic tree of this large enzyme superfamily was obtained from 490 full-length protein sequences. Besides already well-known families of heme b peroxidases arranged in three main structural classes, completely new (hybrid type) peroxidase families are described being located at the border of these classes as well as forming (so far missing) links between them. Hybrid-type A peroxidases represent a minor eukaryotic subfamily from Excavates, Stramenopiles and Rhizaria sharing enzymatic and structural features of ascorbate and cytochrome c peroxidases. Hybrid-type B peroxidases are shown to be spread exclusively among various fungi and evolved in parallel with peroxidases in land plants. In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain. Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily. We present and discuss their phylogeny, sequence signatures and putative biological function.

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Rooted maximum-likelihood tree in a circular polar form reconstructed with 490 full-length sequences from the peroxidase–catalase superfamily. Bootstrap values are presented in a color scheme for the ML output: red >90, violet >70, blue >50, green >30. Three main classes and distinct subfamilies are highlighted. Node labeled as Asterisk is the evolutionary step where the two-domain structure and the bifunctionality were lost (see the discussion in the text). Arrows with number 2 and alphabets indicate the phylogenetic position of particular sequences analyzed in Fig. 2 (with exception of Fig. 2e which is a pseudogene)
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Fig1: Rooted maximum-likelihood tree in a circular polar form reconstructed with 490 full-length sequences from the peroxidase–catalase superfamily. Bootstrap values are presented in a color scheme for the ML output: red >90, violet >70, blue >50, green >30. Three main classes and distinct subfamilies are highlighted. Node labeled as Asterisk is the evolutionary step where the two-domain structure and the bifunctionality were lost (see the discussion in the text). Arrows with number 2 and alphabets indicate the phylogenetic position of particular sequences analyzed in Fig. 2 (with exception of Fig. 2e which is a pseudogene)

Mentions: We have reconstructed a robust phylogenetic tree of the whole peroxidase–catalase superfamily comprising up to 490 full-length protein sequences of members from all known subfamilies. The general presentation of this tree (Fig. 1) clearly distinguishes all three main structural classes already defined by Welinder in 1992 [6]. However, upon closer inspection the occurrence of many so far undescribed clades as well as missing links is obvious.Fig. 1


Turning points in the evolution of peroxidase-catalase superfamily: molecular phylogeny of hybrid heme peroxidases.

Zámocký M, Gasselhuber B, Furtmüller PG, Obinger C - Cell. Mol. Life Sci. (2014)

Rooted maximum-likelihood tree in a circular polar form reconstructed with 490 full-length sequences from the peroxidase–catalase superfamily. Bootstrap values are presented in a color scheme for the ML output: red >90, violet >70, blue >50, green >30. Three main classes and distinct subfamilies are highlighted. Node labeled as Asterisk is the evolutionary step where the two-domain structure and the bifunctionality were lost (see the discussion in the text). Arrows with number 2 and alphabets indicate the phylogenetic position of particular sequences analyzed in Fig. 2 (with exception of Fig. 2e which is a pseudogene)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4232752&req=5

Fig1: Rooted maximum-likelihood tree in a circular polar form reconstructed with 490 full-length sequences from the peroxidase–catalase superfamily. Bootstrap values are presented in a color scheme for the ML output: red >90, violet >70, blue >50, green >30. Three main classes and distinct subfamilies are highlighted. Node labeled as Asterisk is the evolutionary step where the two-domain structure and the bifunctionality were lost (see the discussion in the text). Arrows with number 2 and alphabets indicate the phylogenetic position of particular sequences analyzed in Fig. 2 (with exception of Fig. 2e which is a pseudogene)
Mentions: We have reconstructed a robust phylogenetic tree of the whole peroxidase–catalase superfamily comprising up to 490 full-length protein sequences of members from all known subfamilies. The general presentation of this tree (Fig. 1) clearly distinguishes all three main structural classes already defined by Welinder in 1992 [6]. However, upon closer inspection the occurrence of many so far undescribed clades as well as missing links is obvious.Fig. 1

Bottom Line: In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain.Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily.We present and discuss their phylogeny, sequence signatures and putative biological function.

View Article: PubMed Central - PubMed

Affiliation: Division of Biochemistry, Department of Chemistry, VIBT, Vienna Institute of BioTechnology, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria, marcel.zamocky@boku.ac.at.

ABSTRACT
Heme peroxidases and catalases are key enzymes of hydrogen peroxide metabolism and signaling. Here, the reconstruction of the molecular evolution of the peroxidase-catalase superfamily (annotated in pfam as PF00141) based on experimentally verified as well as numerous newly available genomic sequences is presented. The robust phylogenetic tree of this large enzyme superfamily was obtained from 490 full-length protein sequences. Besides already well-known families of heme b peroxidases arranged in three main structural classes, completely new (hybrid type) peroxidase families are described being located at the border of these classes as well as forming (so far missing) links between them. Hybrid-type A peroxidases represent a minor eukaryotic subfamily from Excavates, Stramenopiles and Rhizaria sharing enzymatic and structural features of ascorbate and cytochrome c peroxidases. Hybrid-type B peroxidases are shown to be spread exclusively among various fungi and evolved in parallel with peroxidases in land plants. In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain. Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily. We present and discuss their phylogeny, sequence signatures and putative biological function.

Show MeSH
Related in: MedlinePlus