Editorial

2 pages, 198 KiB

Open AccessEditorial

Discovering Diverse Roles of Peroxidases and Catalases in Photosynthetic and Non-Photosynthetic Eukaryotes

by Marcel Zámocký

Antioxidants 2022, 11(12), 2337; https://doi.org/10.3390/antiox11122337 - 25 Nov 2022

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This Special Issue of Antioxidants, dedicated to “The Role of Peroxidases and Catalases in Photosynthetic and Non-photosynthetic Eukaryotes“, was accomplished with the contribution of five original research articles and two detailed reviews [...] Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

Research

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16 pages, 15144 KiB

Open AccessArticle

Large-Size Subunit Catalases Are Chimeric Proteins: A H₂O₂ Selecting Domain with Catalase Activity Fused to a Hsp31-Derived Domain Conferring Protein Stability and Chaperone Activity

by Wilhelm Hansberg, Teresa Nava-Ramírez, Pablo Rangel-Silva, Adelaida Díaz-Vilchis and Aydé Mendoza-Oliva

Antioxidants 2022, 11(5), 979; https://doi.org/10.3390/antiox11050979 - 17 May 2022

Cited by 4 | Viewed by 1891

Abstract

Bacterial and fungal large-size subunit catalases (LSCs) are like small-size subunit catalases (SSCs) but have an additional C-terminal domain (CT). The catalytic domain is conserved at both primary sequence and structural levels and its amino acid composition is optimized to select H₂ [...] Read more.

Bacterial and fungal large-size subunit catalases (LSCs) are like small-size subunit catalases (SSCs) but have an additional C-terminal domain (CT). The catalytic domain is conserved at both primary sequence and structural levels and its amino acid composition is optimized to select H₂O₂ over water. The CT is structurally conserved, has an amino acid composition similar to very stable proteins, confers high stability to LSCs, and has independent molecular chaperone activity. While heat and denaturing agents increased Neurospora crassa catalase-1 (CAT-1) activity, a CAT-1 version lacking the CT (C63) was no longer activated by these agents. The addition of catalase-3 (CAT-3) CT to the CAT-1 or CAT-3 catalase domains prevented their heat denaturation in vitro. Protein structural alignments indicated CT similarity with members of the DJ-1/PfpI superfamily and the CT dimers present in LSCs constitute a new type of symmetric dimer within this superfamily. However, only the bacterial Hsp31 proteins show sequence similarity to the bacterial and fungal catalase mobile coil (MC) and are phylogenetically related to MC_CT sequences. LSCs might have originated by fusion of SSC and Hsp31 encoding genes during early bacterial diversification, conferring at the same time great stability and molecular chaperone activity to the novel catalases. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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11 pages, 1322 KiB

Open AccessArticle

The Role of H₂O₂-Scavenging Enzymes (Ascorbate Peroxidase and Catalase) in the Tolerance of Lemna minor to Antibiotics: Implications for Phytoremediation

by Marcelo Pedrosa Gomes, Rafael Shinji Akiyama Kitamura, Raizza Zorman Marques, Marcello Locatelli Barbato and Marcel Zámocký

Antioxidants 2022, 11(1), 151; https://doi.org/10.3390/antiox11010151 - 13 Jan 2022

Cited by 24 | Viewed by 4880

Abstract

We investigated the individual and combined contributions of two distinct heme proteins namely, ascorbate peroxidase (APX) and catalase (CAT) on the tolerance of Lemna minor plants to antibiotics. For our investigation, we used specific inhibitors of these two H₂O₂-scavenging [...] Read more.

We investigated the individual and combined contributions of two distinct heme proteins namely, ascorbate peroxidase (APX) and catalase (CAT) on the tolerance of Lemna minor plants to antibiotics. For our investigation, we used specific inhibitors of these two H₂O₂-scavenging enzymes (p-aminophenol, 3-amino,1,2,4-triazole, and salicylic acid). APX activity was central for the tolerance of this aquatic plant to amoxicillin (AMX), whereas CAT activity was important for avoiding oxidative damage when exposed to ciprofloxacin (CIP). Both monitored enzymes had important roles in the tolerance of Lemna minor to erythromycin (ERY). The use of molecular kinetic approaches to detect and increase APX and/or CAT scavenging activities could enhance tolerance, and, therefore, improve the use of L. minor plants to reclaim antibiotics from water bodies. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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15 pages, 3851 KiB

Open AccessArticle

Comparative Analysis of Three Trypanosomatid Catalases of Different Origin

by Ľubomíra Chmelová, Claretta Bianchi, Amanda T. S. Albanaz, Jana Režnarová, Richard Wheeler, Alexei Yu. Kostygov, Natalya Kraeva and Vyacheslav Yurchenko

Antioxidants 2022, 11(1), 46; https://doi.org/10.3390/antiox11010046 - 26 Dec 2021

Cited by 5 | Viewed by 2397

Abstract

Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene [...] Read more.

Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene transfer from Gammaproteobacteria, extending the list of known bacterial sources of this gene. Comparative biochemical analyses revealed that the enzymes of V. ingenoplastis, Leptomonas pyrrhocoris, and Blastocrithidia sp., representing the three independent catalase-bearing trypanosomatid lineages, have similar properties, except for the unique cyanide resistance in the catalase of the latter species. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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23 pages, 3101 KiB

Open AccessFeature PaperArticle

Agaricales Mushroom Lignin Peroxidase: From Structure–Function to Degradative Capabilities

by María Isabel Sánchez-Ruiz, Iván Ayuso-Fernández, Jorge Rencoret, Andrés Manuel González-Ramírez, Dolores Linde, Irene Davó-Siguero, Antonio Romero, Ana Gutiérrez, Angel T. Martínez and Francisco Javier Ruiz-Dueñas

Antioxidants 2021, 10(9), 1446; https://doi.org/10.3390/antiox10091446 - 12 Sep 2021

Cited by 13 | Viewed by 3634

Abstract

Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of [...] Read more.

Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H₂O₂, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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13 pages, 4068 KiB

Open AccessArticle

Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida

by Fernanda Lazzarotto, Paloma Koprovski Menguer, Luiz-Eduardo Del-Bem, Marcel Zámocký and Márcia Margis-Pinheiro

Antioxidants 2021, 10(4), 597; https://doi.org/10.3390/antiox10040597 - 13 Apr 2021

Cited by 12 | Viewed by 3823

Abstract

Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases [...] Read more.

Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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Review

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28 pages, 4832 KiB

Open AccessReview

Monofunctional Heme-Catalases

by Wilhelm Hansberg

Antioxidants 2022, 11(11), 2173; https://doi.org/10.3390/antiox11112173 - 02 Nov 2022

Cited by 8 | Viewed by 2407

Abstract

The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H₂O₂) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one [...] Read more.

The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H₂O₂) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one of the issues examined. Part of the answer is a gate valve system that is instrumental to drive out solvent molecules from the final section of the main channel. A second issue relates to how the enzyme deals with an unproductive reactive compound I (Cpd I) intermediate. Peroxidatic two and one electron donors and the transfer of electrons to the active site from NADPH and other compounds are reviewed. The new ascribed catalase reactions are revised, indicating possible measurement pitfalls. A third issue concerns the heme b to heme d oxidation, why this reaction occurs only in some large-size subunit catalases (LSCs), and the possible role of singlet oxygen in this and other modifications. The formation of a covalent bond between the proximal tyrosine with the vicinal residue is analyzed. The last issue refers to the origin and function of the additional C-terminal domain (TD) of LSCs. The TD has a molecular chaperone activity that is traced to a gene fusion between a Hsp31-type chaperone and a small-size subunit catalase (SSC). Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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18 pages, 1861 KiB

Open AccessReview

Plant Glutathione Peroxidases: Non-Heme Peroxidases with Large Functional Flexibility as a Core Component of ROS-Processing Mechanisms and Signalling

by Krisztina Bela, Riyazuddin Riyazuddin and Jolán Csiszár

Antioxidants 2022, 11(8), 1624; https://doi.org/10.3390/antiox11081624 - 21 Aug 2022

Cited by 14 | Viewed by 3323

Abstract

Glutathione peroxidases (GPXs) are non-heme peroxidases catalyzing the reduction of H₂O₂ or organic hydroperoxides to water or corresponding alcohols using glutathione (GSH) or thioredoxin (TRX) as a reducing agent. In contrast to animal GPXs, the plant enzymes are non-seleno monomeric [...] Read more.

Glutathione peroxidases (GPXs) are non-heme peroxidases catalyzing the reduction of H₂O₂ or organic hydroperoxides to water or corresponding alcohols using glutathione (GSH) or thioredoxin (TRX) as a reducing agent. In contrast to animal GPXs, the plant enzymes are non-seleno monomeric proteins that generally utilize TRX more effectively than GSH but can be a putative link between the two main redox systems. Because of the substantial differences compared to non-plant GPXs, use of the GPX-like (GPXL) name was suggested for Arabidopsis enzymes. GPX(L)s not only can protect cells from stress-induced oxidative damages but are crucial components of plant development and growth. Due to fine-tuning the H₂O₂ metabolism and redox homeostasis, they are involved in the whole life cycle even under normal growth conditions. Significantly new mechanisms were discovered related to their transcriptional, post-transcriptional and post-translational modifications by describing gene regulatory networks, interacting microRNA families, or identifying Lys decrotonylation in enzyme activation. Their involvement in epigenetic mechanisms was evidenced. Detailed genetic, evolutionary, and bio-chemical characterization, and comparison of the main functions of GPXs, demonstrated their species-specific roles. The multisided involvement of GPX(L)s in the regulation of the entire plant life ensure that their significance will be more widely recognized and applied in the future. Full article

(This article belongs to the Special Issue The Role of Peroxidases and Catalases in Photosynthetic and Non–photosynthetic Eukaryotes)

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