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Plant Glutathione Peroxidases: Comparison
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Please note this is a comparison between Version 2 by Vivi Li and Version 1 by Riyazuddin Riyazuddin.

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. 

  • antioxidants
  • glutathione peroxidases
  • growth
  • reactive oxygen species
  • redox status
  • stress responses
  • thiol peroxidases

1. Introduction

The generation of reactive oxygen species (ROS), such as superoxide radical (O2•−), hydrogen peroxide (H2O2), singlet oxygen (1O2), and hydroxyl radical (OH•), is a by-product of aerobic life. These highly reactive compounds are constantly produced, essentially by respiratory and photosynthetic electron transport chains, and can react with biomolecules including lipids, proteins, and nucleic acids [1][2]. ROS and reactive nitrogen species (RNS) may trigger several post-translational modifications, such as disulfide bond formation, thiol oxidation to sulfenic/sulfinic/sulfonic acid, glutathionylation or nitrosylation. Since an elevated ROS level can trigger damage or irreversible effects on development of tissues and organs, different non-enzymatic antioxidants (such as ascorbate, glutathione, carotenoids, tocopherols) and ROS-processing enzymes have evolved in aerobic organisms [2].
The extremely widespread and diversified H2O2 decomposing peroxidases (EC.1.11.1.x) are present in all living organisms (reviewed, e.g., in [3]). They can be grouped based on the heme cofactor [4][5]. According to the RedoxiBase database, more than 80% of known peroxidase genes code heme peroxidases (https://peroxibase.toulouse.inra.fr, accessed on 22 June 2022). In plants, the most widely known peroxidases—such as the ascorbate peroxidase and catalase belonging to the intracellular Class I peroxidases and guaiacol peroxidases, the Class III peroxidases secreted to the extracellular space or transported into the vacuole—are heme-containing enzymes that are in the peroxidase-catalase superfamily [3][4][6]. The importance of non-heme peroxidases has emerged in the last decades [7][8][9]. The non-heme peroxidases comprise thiol peroxidases, alkylhydroperoxidase, haloperoxidases, NADH peroxidases and the pseudocatalase manganese catalases; but only the members of thiol peroxidase superfamily have been described in plants (Figure 1)  [4][6] (https://peroxibase.toulouse.inra.fr, accessed on 22 June 2022). Among them, the ubiquitous thiol peroxidases serve both as ROS scavengers and contributors of ROS signalling. They are divided into two main enzyme families: peroxiredoxins (PRXs) or thioredoxin peroxidases, and glutathione peroxidases (mostly abbreviated as GPXs or GPxs).
GPXs (EC 1.11.1.9 for classical glutathione peroxidase and EC 1.11.1.12, phospholipid-hydroperoxide glutathione peroxidase) differ substantially both for the oxidizing peroxides and the reducing substrates [10]. They catalyze the reduction of H2O2 or organic hydroperoxides to water or corresponding alcohols and oxidize reduced glutathione (GSH, γ-Glu-Cys-Gly) or thioredoxin (TRX) [11][12]. The first GPX was discovered in erythrocytes [13], but later several GPXs were described in all estimated eukaryotic organisms. Some of the GPX isoenzymes contain the highly reactive selenocysteine (SeCys) residue in their active site, while others contain Cys [14]. Both the seleno- or nonseleno GPXs are considered to be central components of ROS-processing mechanisms in animals [12][15]. Mammals harbour eight GPX isoenzymes (GPX1-8), of which five (GPX1-4 and GPX6 in human) contain SeCys in their active site, and three (GPX5, GPX7, and GPX8) employ active-site cysteines [16][17][18]. They are crucial players in many biological processes, such as fertility, anti-inflammatory and anti-carcinogenesis associated routes [17][19][20]. It was suggested that the convergent expansion of mammalian GPXs in independent lineages might be important for avoiding oxidative damages and the adaption to stressful environments [21]. GPX4, otherwise called phospholipid hydroperoxide glutathione peroxidase (PHGPX) and originally peroxidation inhibiting protein (PIP), participates especially in the maintenance of membrane integrity due to decreasing the amount of lipid peroxides, and it has key role in the regulation of ferroptosis [22][23][24].
The plant GPXs exhibit the highest homology to the animal GPX4 isoenzyme; however, the plant enzymes contain Cys instead of SeCys in their active site and generally prefer the TRX regenerating system rather than GSH [8][16][25][26]. Due to their structural similarity to animal GPXs, but different activities and substrate specificities, the glutathione peroxidase-like (GPXL) name was suggested for the Arabidopsis thaliana GPX isoenzymes [27]. Besides keeping low ROS level, the ROS-processing antioxidant enzymes may even sense and signal ROS availability and redox perturbations [28]. They are involved in control of ROS gradients e.g., in the maintenance of stem cell niche or triggering differentiation in the shoot and root apical meristems (SAM and RAM, respectively), and in the proper zygote/embryo development [29][30][31][32]. In addition, using GSH and/or TRX as a reductant, the GPX(L)s influence the redox status of these main redox compounds. They can modify the thiol/disulfide balance and protein activity and moreover were considered to function as redox sensors by linking ROS to functional redox signalling [26][33][34][35][36].

2. Phylogenetic Aspects of Plant GPXs

Since the GPXs present no linear evolution, and non-animal GPXs are very distinct from most vertebrate GPXs, the original ancestor of the GPX gene family is uncertain [14][16]. Based on through robust phylogenetic studies and sequence analyses, Trenz et al. proposed that all GPX-encoding genes share a monomeric common ancestor and the bacterial, animal and the TRX-applying fungal and plant GPXs diverged early in evolution and diversified independently in different kingdoms and phyla [14]. This might explain the findings that, e.g., the Tetrahymena thermophila, a unicellular eukaryote (a ciliate) genome contains 12 GPX genes [37], but the Chlamydomonas reinhardtii unicellular green alga employs two SeCys-containing GPXs and three non-selenium GPXs (GPX3-5) [9][38]. Phylogenetic studies of GPX genes from different plant species showed that their number varies between 2 and 25 [39][40][41]. For example, two GPX genes were identified in Physcomitrella patens [39] and Panax ginseng [42], three in Hordeum vulgare [43] and Vigna radiata [44], four in Pinus tabulaeformis [45] and Brachypodium distachyon [39], and five genes in Oryza sativa [15][39], Phoenix dactylifera (date palm) [46], Populus trichocarpa [25], Ricinus communis [47], and Solanum lycopersicum [39]. Six GPXs are encoded by Cucumis sativus [48], Citrullus lanatus [49] and Lotus japonica [50] genome, seven genes were found in Sorghum bicolor [51] and Zea mays [52], while there are eight in Arabidopsis thaliana [53] and Brassica oleracea [40]. It was concluded that GPX genes showed duplication events in many plant species, e.g., in Arabidopsis [53] and maize [52]. In most of the cases, a relatively higher number of GPX genes was found in plants with polyploid genome [54]. For example, 12 genes were identified in Brassica rapa [40] and Triticum aestivum [55], 13 in Gossypium hirsutum [54] and Glycine max [44], and 25 GPX genes in Brassica napus [40]. According to the conserved domain and gene structure analyses conducted on GPX(L) genes from various species, the plant GPXs can be categorized into four or five main groups [44][47][52][54][55][56][57][58]. Comparison of GPX genes belonging to distinct groups disclosed highly similar motifs and conserved exon-intron arrangement patterns within each group [52]. This indicates that their structure and function might have been preserved during evolution, yet several differences were also discovered, like in R. communis and Z. maize [47][52]. Generally, the number of exons ranges between four to six, and introns numbers varied from four to ten but showed significant variability among species (e.g., [44][52][54][55][58]. Deviations might be assigned to gene and whole-genome duplications. Evidence of tandem or segmental duplications has been found at several plant GPXs [39][40][44][52][53]. It was suggested that the gene replication activities might play a crucial role in gene evolution [40].

3. Structure, Biochemical Properties, and Main Activities of Plant GPX Proteins

Plant GPXs are monomeric proteins (Table 1). The conserved protein structure of GPXs consists of central β-sheets surrounded by α-helices [59]. Most of the mammalian GPXs possess an oligomerization loop between the α3 helix and β6 strand, and consequently they form dimers or tetramers [60], however the monomer mammalian GPX4 (PHGPX) and plant GPXs do not contain any oligomerization loop. Although it was reported that P. trichocarpa GPX5 can also form a dimer, in this case the dimerization occurs due to non-covalent bonds with the help of hydrophobic and aromatic residues [59]. Sub-cellular localization analyses in various species revealed that the GPXs are localized in chloroplasts, mitochondria, cytoplasmic, extracellular and nuclear regions [15][51][52][54][55]. Although it was proposed that in other cellular compartments, such as peroxisomes and endoplasmic reticulum (ER), other antioxidant enzymes are the main ROS scavengers [52], Attacha et al. proved that AtGPXL3 is a luminal protein that can be anchored to the ER and Golgi membranes [27]. The presence of a transmembrane domain was reported too for example in corn ZmGPX4 enzyme [52]. The catalytic mechanism of glutathione peroxidases is the following:
2 GSH + H
2
O
2
 → glutathione disulfide + 2 H
2
O
 
2 GSH + lipid hydroperoxide → glutathione disulfide + lipid + 2 H
2
O
 
It was suggested that the monomer structure allows the direct reduction of membrane-bound lipid peroxides [19][61], thus the main proposed role of plant GPXs was in the maintenance of membrane integrity, especially under different stress conditions. Recent results of the molecular docking studies performed on maize proteins with three lipid hydroperoxides also strengthen this function [52]. Interestingly, the reduction activity of purified Arabidopsis, sunflower, and tomato GPXs with H2O2 were similar or even 2–7-times higher than those with organic hydroperoxides using Escherichia coli TRX [26][62]. In contrary to the yeast GPX, among the investigated recombinant plant GPXs (AtGPXL1, −2, −5, −6, HaGPX1, SlGPX1 and one B. rapa GPX) none of them utilized GSH for reduction of H2O2. These enzymes showed generally higher preference towards lipid hydroperoxides as electron acceptors and, except for A. thaliana and B. rapa  GPX(L)s, they accepted GSH as electron donor (Table 1), but showed very low activity [26][62]. These results, together with the similar function of GPXs in model and crop plants (detailed later in Section 4 and Section 5) may justify the use of the GPXL name and abbreviation for all plant GPX proteins [27][63]. Interestingly, the levels of the lipid peroxidation marker malondialdehyde (MDA) and/or H2O2 were increased in several Arabidopsis gpxl mutants [64][65][66], indicating that these enzymes in vivo participate both in conversion of lipid hydroperoxides to less toxic molecules and are involved in the H2O2 homeostasis. During the reduction of peroxides, the catalytic CysP-S- is oxidized to a sulfenic acid (CysP-SOH). The main difference between the distinct classes of non-heme peroxidases is the mechanism of regeneration of the CysP-SOH, which can be reduced directly (1-Cys mechanism) or by involving a second, so-called resolving Cys residue (CysR-SH) of the enzyme (2-Cys catalytic cycle) [7]. Trenz et al. suggested that the ancestral GPX protein contained both the peroxidatic and resolving cysteines [14]. In plant GPXs, the sulfenic acid forms an intramolecular disulfide with a second Cys. However, beside the two catalytic cysteines, the plant GPXs contain a third conserved Cys residue outside of the classical catalytic site, but its function is still not clear. In some cases, both the second and the third Cys can be responsible for disulfide bridge formation, as it was reported in Chinese cabbage [67], while in poplar the third Cys is the resolving type [25]; nevertheless, these are not general features of plant GPXs. The 2-Cys disulfide can be reduced by GSH or by TRX [68]. Kinetic characterization of recombinant proteins originating from diverse sources revealed that the activity (depending on the used peroxide substrates and plants) was much higher in the presence of TRX than that of GSH [25][26][62][67]. The investigated Arabidopsis enzymes were able to reduce the peroxide only with TRX [26]. The intramolecular rearrangement, catalytic cycle and regeneration of plant GPXs are similar to that of the peroxiredoxins, thus they were even suggested to be considered as the fifth group of PRXs [7][25]. In vivo activity measurements conducted on different Arabidopsis T-DNA insertion mutants revealed that the single mutation of AtGPXL genes could significantly decrease the TRX activity especially in shoots both under control conditions and after applying salt stress [63]. Interestingly, in the AtGPXL5 overexpressing plants (OX-AtGPXL5), the glutathione peroxidase and thioredoxin peroxidase activities (GPOX and TPOX, respectively) were not elevated compared to the wild type under the above conditions [66][69]. It should be noted that the most numerous, plant-specific classes of the diverse glutathione transferase (GST) enzyme family exhibit more GSH-dependent peroxidase activities than GPXs against H2O2 and organic peroxides [70]. In addition, GPXs possess some functional overlaps with the PRXs, thus GPXs were suggested to be a putative link between the glutathione- and the thioredoxin-based detoxifying systems [53][56][67]. However, the involvement of GPXs is indicated not only in ROS detoxification but also in protection of cellular redox homeostasis by regulation of the thiol/disulfide balance and protein functions [26]. Meyer et al. [56] proposed that thiol peroxidases link ROS to functional redox signalling [36]. GPXs can oxidase Cys-containing proteins involved in the signalling, such as phosphatases, kinases, and transcription factors, thus regulating different pathways [26][56][71][72]. Even more, the significance of ER-localized GPXL3 in oxidative protein folding, in disulfide bridge formation and/or regeneration of the participant enzymes, at the same time processing the H2O2 arose locally, were implicated [27][36]. As a summation, plant GPXs might have innumerable roles in stress tolerance and development [41].

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