Unexpected diversity of dye-decolorizing peroxidases

Abstract

Dye-decolorizing peroxidase (DyP)-type peroxidases are a family of heme-containing peroxidases. Because DyP-type peroxidases can degrade recalcitrant anthraquinone dyes and lignin, their potential applications in the treatment of wastewater containing dyes and lignin degradation are expected. Although many DyP-type peroxidases have been characterized experimentally, most of the reported DyP-type peroxidases are from basidiomycetous fungi and bacteria. Therefore, the taxonomic distribution of the DyP-type peroxidases remains unclear. In this study, we analyzed the phylogenetic tree using all DyP-type peroxidase sequences available in the InterPro database. The findings mainly divided this family into three classes. Metazoa and Archaea also have the genes coding for DyP-type peroxidases, and the sequences belonging to two subclasses have the pyruvate formate lyase or cytochrome P450 domain in addition to the DyP domain. This study reveals differences in the conservation of important residues among classes. The findings will accelerate research on the DyP-type peroxidase family.

Keywords: DyP; DyP, Dye-decolorizing peroxidase; Dye-decolorizing peroxidase; PDB, Protein Data Bank; Peroxidase; Phylogenetic analysis.

Fig. 1

Phylogenetic tree. Each branch is color coded by organism of origin. Numbers in parentheses denote the branch numbers of each organism. SH-aLRT (>80%) and Ultrafast bootstrap support (>95%) values are indicated by circles on nodes. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

Reformatted view of the tree in Fig. 1. (a) Each branch is color coded by organism of origin as in Fig. 1. Branch lengths are ignored. Circle I shows the existence of the domains except DyP domain. Representative domain structures are shown in (b). Circle II shows the classification as shown in (c). Circle III shows the amino acid sequence lengths of each sequence as concentrical bar graph as shown in (d). Circle IV is the known DyP-type peroxidase mapping. Each DyP name and organism of origin are listed in (e). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Comparison of overall structures, heme active site residues, and active radical sites among subclasses. (a) Known structure and predicted structures of unexplored subclasses. Top: DyP name or UniProt IDs and the organisms of origins; Middle: overall structures. Heme active site residues and candidates of active radical sites are shown as stick and sphere models, respectively; Bottom: close-up views of heme active sites. DyP from B. adusta are shown in black box as representative known structure (PDB ID: 3afv). Residues “d1–4″ and underlined “p1–3″ denote the important residues of heme distal and proximal sides, respectively. In subclasses I1, I2, P1, and P2, the predicted structures by AlphaFold were downloaded from UniProt database. In subclass V4, the structure was predicted by ColabFold coupled with Google Colaboratory [39]. (b) Sequence logo representations of the occurrences of amino acid residues of heme active site. Active site residues are highlighted in grey and the adjacent residues are shown. Vertical axes show bits from 0 to 5. The sequence logos were generated using the WebLogo 3 program [40]. (c) Sequence logo representations of the occurrences of amino acid residues of candidates of active radical sites.