Limits...
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.

Show MeSH

Related in: MedlinePlus

Multiple sequence alignment presenting peroxidase-like genes coding for variants of plant ascorbate peroxidase-like proteins that most probably lack the heme group. Sequences are compared with functional ascorbate peroxidases from P. sativum (PsAPx) and yeast cytochrome c peroxidase (SceCcP) with known 3D structures. a Region of residues around distal histidine. b Region of residues around proximal histidine. Parameters for the alignment are described in the Sect. “Materials and methods”. Abbreviations of peroxidase names are taken from PeroxiBase
© Copyright Policy - OpenAccess
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4232752&req=5

Fig6: Multiple sequence alignment presenting peroxidase-like genes coding for variants of plant ascorbate peroxidase-like proteins that most probably lack the heme group. Sequences are compared with functional ascorbate peroxidases from P. sativum (PsAPx) and yeast cytochrome c peroxidase (SceCcP) with known 3D structures. a Region of residues around distal histidine. b Region of residues around proximal histidine. Parameters for the alignment are described in the Sect. “Materials and methods”. Abbreviations of peroxidase names are taken from PeroxiBase

Mentions: The present analysis has also shown that several APx genes in Chlorophyta and higher plants lack most of the essential residues for heme binding and/or catalysis (Fig. 6a, b). This is in contrast to the hybrid-type A2 peroxidase from Euglena gracilis (EgrAPx-CcP1) with its unique structure of two functional domains [40]. This leads us to the hypothesis that right at the level of segregation from bifunctional KatGs to monofunctional peroxidases (labeled with * in Fig. 1) the two-domain version might have existed for some time before being separated and loosing functionality (Fig. 6). The occurrence of separated (heme-free) KatG-like C-terminal domains still present in some genomes (cf. PeroxiBase) supports this hypothesis.Fig. 6


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)

Multiple sequence alignment presenting peroxidase-like genes coding for variants of plant ascorbate peroxidase-like proteins that most probably lack the heme group. Sequences are compared with functional ascorbate peroxidases from P. sativum (PsAPx) and yeast cytochrome c peroxidase (SceCcP) with known 3D structures. a Region of residues around distal histidine. b Region of residues around proximal histidine. Parameters for the alignment are described in the Sect. “Materials and methods”. Abbreviations of peroxidase names are taken from PeroxiBase
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Multiple sequence alignment presenting peroxidase-like genes coding for variants of plant ascorbate peroxidase-like proteins that most probably lack the heme group. Sequences are compared with functional ascorbate peroxidases from P. sativum (PsAPx) and yeast cytochrome c peroxidase (SceCcP) with known 3D structures. a Region of residues around distal histidine. b Region of residues around proximal histidine. Parameters for the alignment are described in the Sect. “Materials and methods”. Abbreviations of peroxidase names are taken from PeroxiBase
Mentions: The present analysis has also shown that several APx genes in Chlorophyta and higher plants lack most of the essential residues for heme binding and/or catalysis (Fig. 6a, b). This is in contrast to the hybrid-type A2 peroxidase from Euglena gracilis (EgrAPx-CcP1) with its unique structure of two functional domains [40]. This leads us to the hypothesis that right at the level of segregation from bifunctional KatGs to monofunctional peroxidases (labeled with * in Fig. 1) the two-domain version might have existed for some time before being separated and loosing functionality (Fig. 6). The occurrence of separated (heme-free) KatG-like C-terminal domains still present in some genomes (cf. PeroxiBase) supports this hypothesis.Fig. 6

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