Mutational and structural analysis of an ancestral fungal dye‐decolorizing peroxidase

Zitare, Ulises A.; Habib, M. Hadj; Rozeboom, H.J.; Mascotti, María Laura; Todorović, Smilja; Fraaije, Marco W.

doi:10.1111/febs.15687

Cited by 15 publications

(11 citation statements)

References 69 publications

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“…Additionally, it has been reported that the distal aspartic acid of ElDyP (class P) is catalytically more important than the distal arginine and plays a key role in determining the acidic pH optimum of DyPs [ 20 ]. Similar effect depending on pH has been reported in a resurrect class V DyP [ 60 ].…”

Section: Importance Of Tertiary Structure and Catalytic Mechanismsupporting

confidence: 84%

DyP-Type Peroxidases: Recent Advances and Perspectives

Sugano

Yoshida

2021

IJMS

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In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.

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Section: Importance Of Tertiary Structure and Catalytic Mechanismsupporting

confidence: 84%

DyP-Type Peroxidases: Recent Advances and Perspectives

Sugano

Yoshida

2021

IJMS

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“…Mn +2 oxidation sites described in bacterial C-type DyPs were not found to be conserved in IrlacDyP structure either [57,58]. On the other hand, the ability to oxidize Mn 2+ in a resurrected basidiomycete D-type DyP has recently been reported, although a Mn 2+ -binding site was not found in this enzyme [59]. Thus, Mn 2+ oxidation sites do not seem to be conserved in DyPs and MnP, neither between type C and type D DyPs, nor even between type D DyPs.…”

Section: Structural Model Of the Irpex Lacteus Recombinant Dypmentioning

confidence: 81%

Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates

Eugenio

Peces-Pérez

Linde

et al. 2021

JoF

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A dye-decolorizing peroxidase (DyP) from Irpex lacteus was cloned and heterologously expressed as inclusion bodies in Escherichia coli. The protein was purified in one chromatographic step after its in vitro activation. It was active on ABTS, 2,6-dimethoxyphenol (DMP), and anthraquinoid and azo dyes as reported for other fungal DyPs, but it was also able to oxidize Mn2+ (as manganese peroxidases and versatile peroxidases) and veratryl alcohol (VA) (as lignin peroxidases and versatile peroxidases). This corroborated that I. lacteus DyPs are the only enzymes able to oxidize high redox potential dyes, VA and Mn+2. Phylogenetic analysis grouped this enzyme with other type D-DyPs from basidiomycetes. In addition to its interest for dye decolorization, the results of the transformation of softwood and hardwood lignosulfonates suggest a putative biological role of this enzyme in the degradation of phenolic lignin.

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“…Another in silico source for enzyme identification is ancestral sequence reconstruction (ASR) By obtaining the possible ancestral sequence, novel enzymes can be identified via homology searches or novel proteins can be expressed by the creation of fusion proteins ( Verma et al, 2019 ; Zitare et al, 2021 ). In addition, ASR provides insights into the evolutionary development of enzymes ( Ruiz-Dueñas et al, 2020 ).…”

Section: The Search For New Plastics Degrading Microbes and Enzymesmentioning

confidence: 99%

Toward Microbial Recycling and Upcycling of Plastics: Prospects and Challenges

2022

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Annually, 400 Mt of plastics are produced of which roughly 40% is discarded within a year. Current plastic waste management approaches focus on applying physical, thermal, and chemical treatments of plastic polymers. However, these methods have severe limitations leading to the loss of valuable materials and resources. Another major drawback is the rapid accumulation of plastics into the environment causing one of the biggest environmental threats of the twenty-first century. Therefore, to complement current plastic management approaches novel routes toward plastic degradation and upcycling need to be developed. Enzymatic degradation and conversion of plastics present a promising approach toward sustainable recycling of plastics and plastics building blocks. However, the quest for novel enzymes that efficiently operate in cost-effective, large-scale plastics degradation poses many challenges. To date, a wide range of experimental set-ups has been reported, in many cases lacking a detailed investigation of microbial species exhibiting plastics degrading properties as well as of their corresponding plastics degrading enzymes. The apparent lack of consistent approaches compromises the necessary discovery of a wide range of novel enzymes. In this review, we discuss prospects and possibilities for efficient enzymatic degradation, recycling, and upcycling of plastics, in correlation with their wide diversity and broad utilization. Current methods for the identification and optimization of plastics degrading enzymes are compared and discussed. We present a framework for a standardized workflow, allowing transparent discovery and optimization of novel enzymes for efficient and sustainable plastics degradation in the future.

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Mutational and structural analysis of an ancestral fungal dye‐decolorizing peroxidase

Cited by 15 publications

References 69 publications

DyP-Type Peroxidases: Recent Advances and Perspectives

DyP-Type Peroxidases: Recent Advances and Perspectives

Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates

Toward Microbial Recycling and Upcycling of Plastics: Prospects and Challenges

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