Unexpected Diversity of Dye-decolorizing Peroxidases

Overview

Journal Biochem Biophys Rep

Specialty Biochemistry

Date 2022 Dec 8

PMID 36478894

Authors

Toru Yoshida

Yasushi Sugano

Affiliations

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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.

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References

Shrestha R, Chen X, Ramyar K, Hayati Z, Carlson E, Bossmann S . Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from . ACS Catal. 2018; 6(12):8036-8047. PMC: 5751956. DOI: 10.1021/acscatal.6b01952. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Lien K, Dinshaw K, Nichols R, Cassidy-Amstutz C, Knight M, Singh R . A nanocompartment system contributes to defense against oxidative stress in . Elife. 2021; 10. PMC: 8635971. DOI: 10.7554/eLife.74358. View

Roberts J, Singh R, Grigg J, Murphy M, Bugg T, Eltis L . Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1. Biochemistry. 2011; 50(23):5108-19. DOI: 10.1021/bi200427h. View

Minh B, Schmidt H, Chernomor O, Schrempf D, Woodhams M, von Haeseler A . IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020; 37(5):1530-1534. PMC: 7182206. DOI: 10.1093/molbev/msaa015. View

Kimani V, Ullrich R, Buttner E, Herzog R, Kellner H, Jehmlich N . First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by . Biomolecules. 2021; 11(9). PMC: 8469222. DOI: 10.3390/biom11091391. View

Sugawara K, Igeta E, Amano Y, Hyuga M, Sugano Y . Degradation of antifungal anthraquinone compounds is a probable physiological role of DyP secreted by Bjerkandera adusta. AMB Express. 2019; 9(1):56. PMC: 6478788. DOI: 10.1186/s13568-019-0779-4. View

Mendes S, Brissos V, Gabriel A, Catarino T, Turner D, Todorovic S . An integrated view of redox and catalytic properties of B-type PpDyP from Pseudomonas putida MET94 and its distal variants. Arch Biochem Biophys. 2015; 574:99-107. DOI: 10.1016/j.abb.2015.03.009. View

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

10.

Sugano Y, Muramatsu R, Ichiyanagi A, Sato T, Shoda M . DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases. J Biol Chem. 2007; 282(50):36652-8. DOI: 10.1074/jbc.M706996200. View

11.

Kaur A, Van P, Busch C, Robinson C, Pan M, Pang W . Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol. 2010; 6:393. PMC: 2925529. DOI: 10.1038/msb.2010.50. View

12.

Linde D, Pogni R, Canellas M, Lucas F, Guallar V, Baratto M . Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J. 2014; 466(2):253-62. PMC: 4357238. DOI: 10.1042/BJ20141211. View

13.

Horitani M, Shisler K, Broderick W, Hutcheson R, Duschene K, Marts A . Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond. Science. 2016; 352(6287):822-5. PMC: 4929858. DOI: 10.1126/science.aaf5327. View

14.

Rai A, Klare J, Reinke P, Englmaier F, Fohrer J, Fedorov R . Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from . Int J Mol Sci. 2021; 22(12). PMC: 8230527. DOI: 10.3390/ijms22126265. View

15.

Knappe J, Sawers G . A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol Rev. 1990; 6(4):383-98. DOI: 10.1111/j.1574-6968.1990.tb04108.x. View

16.

Poulos T . Heme enzyme structure and function. Chem Rev. 2014; 114(7):3919-62. PMC: 3981943. DOI: 10.1021/cr400415k. View

17.

Sugano Y, Yoshida T . DyP-Type Peroxidases: Recent Advances and Perspectives. Int J Mol Sci. 2021; 22(11). PMC: 8197335. DOI: 10.3390/ijms22115556. View

18.

Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M . ColabFold: making protein folding accessible to all. Nat Methods. 2022; 19(6):679-682. PMC: 9184281. DOI: 10.1038/s41592-022-01488-1. View

19.

Uchida T, Sasaki M, Tanaka Y, Ishimori K . A Dye-Decolorizing Peroxidase from Vibrio cholerae. Biochemistry. 2015; 54(43):6610-21. DOI: 10.1021/acs.biochem.5b00952. View

20.

Savelli B, Li Q, Webber M, Jemmat A, Robitaille A, Zamocky M . RedoxiBase: A database for ROS homeostasis regulated proteins. Redox Biol. 2019; 26:101247. PMC: 6597783. DOI: 10.1016/j.redox.2019.101247. View