Crystal structure analysis of peroxidase from the palm tree Chamaerops excelsa

Class III plant peroxidases: From classification to physiological functions

Peroxidases (EC 1.11.1.7) are involved in a wide range of physiological processes, hence their broad distribution across biological systems. These proteins can be classified as haem or non-haem enzymes. According to the RedOxiBase database, haem peroxidases are approximately 84 % of all known peroxidase enzymes. Class III plant peroxidases are haem-enzymes that share similar three-dimensional structures and a common catalytic mechanism for hydrogen peroxide degradation. They exist as large multigene families and are involved in metabolizing Reactive Oxygen Species (ROS), hormone synthesis and decomposition, fruit growth, defense, and cell wall synthesis and maintenance. As a result, plant peroxidases gained attention in research and became one of the most extensively studied groups of enzymes. This review provides an update on the database, classification, phylogeny, mechanism of action, structure, and physiological functions of class III plant peroxidases.

Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple

The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.

Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements

Unspecific peroxygenases (UPOs) are extracellular fungal enzymes of biotechnological interest as self-sufficient (and more stable) counterparts of cytochrome P450 monooxygenases, the latter being present in most living cells. Expression hosts and structural information are crucial for exploiting UPO diversity (over eight thousand UPO-type genes were identified in sequenced genomes) in target reactions of industrial interest. However, while many thousands of entries in the Protein Data Bank include molecular coordinates of P450 enzymes, only 19 entries correspond to UPO enzymes, and UPO structures from only two species (Agrocybe aegerita and Hypoxylon sp.) have been published to date. In the present study, two UPOs from the basidiomycete Marasmius rotula (rMroUPO) and the ascomycete Collariella virescens (rCviUPO) were crystallized after sequence optimization and Escherichia coli expression as active soluble enzymes. Crystals of rMroUPO and rCviUPO were obtained at sufficiently high resolution (1.45 and 1.95 Å, respectively) and the corresponding structures were solved by molecular replacement. The crystal structures of the two enzymes (and two mutated variants) showed dimeric proteins. Complementary biophysical and molecular biology studies unveiled the diverse structural bases of the dimeric nature of the two enzymes. Intermolecular disulfide bridge and parallel association between two α-helices, among other interactions, were identified at the dimer interfaces. Interestingly, one of the rCviUPO variants incorporated the ability to produce fatty acid diepoxides—reactive compounds with valuable cross-linking capabilities—due to removal of the enzyme C-terminal tail located near the entrance of the heme access channel. In conclusion, different dimeric arrangements could be described in (short) UPO crystal structures.

Air pollution particles hijack peroxidasin to disrupt immunosurveillance and promote lung cancer

Although fine particulate matter (FPM) in air pollutants and tobacco smoke is recognized as a strong carcinogen and global threat to public health, its biological mechanism for inducing lung cancer remains unclear. Here, by investigating FPM's bioactivities in lung carcinoma mice models, we discover that these particles promote lung tumor progression by inducing aberrant thickening of tissue matrix and hampering migration of antitumor immunocytes. Upon inhalation into lung tissue, these FPM particles abundantly adsorb peroxidasin (PXDN) - an enzyme mediating type IV collagen (Col IV) crosslinking - onto their surface. The adsorbed PXDN exerts abnormally high activity to crosslink Col IV via increasing the formation of sulfilimine bonds at the NC1 domain, leading to an overly dense matrix in the lung tissue. This disordered structure decreases the mobility of cytotoxic CD8+ T lymphocytes into the lung and consequently impairs the local immune surveillance, enabling the flourishing of nascent tumor cells. Meanwhile, inhibiting the activity of PXDN abolishes the tumor-promoting effect of FPM, indicating the key impact of aberrant PXDN activity on the tumorigenic process. In summary, our finding elucidates a new mechanism for FPM-induced lung tumorigenesis and identifies PXDN as a potential target for treatment or prevention of the FPM-relevant biological risks.

Phenoloxidases in Plants-How Structural Diversity Enables Functional Specificity

The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases (LACs), we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed LAC functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.

Crystal Structure Analysis of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites

Proso millet peroxidase (PmPOD) belongs to class III plant peroxidases, which are enzymes typically characterized by their heme coenzymes. PmPOD exhibits not only heme-dependent peroxidase activity but also heme-independent phosphatase activity. Crystal structure analysis and sequence alignment showed that PmPOD contained a phosphatase catalytic loop CXXXXXR in its β-domain that is similar to the active site of a dual-specific phosphatase. Recombinant truncated proso millet peroxidase (tPmPOD), which contained only a conserved catalytic loop CXXXXXR of phosphatase, was found to exhibit phosphatase activity. Five tPmPOD mutants containing five different mutations in the phosphatase active sites exhibited significantly lower phosphatase activity compared to that of tPmPOD, indicating that the five amino acids play important roles in the phosphatase activity of tPmPOD. Finally, nucleophilic amino acid Cys192 formed a disulfide bond with Cys219 to protect the stability of a sulfhydryl group; thus, it may play a decisive role in the phosphatase activity of PmPOD.

Comparison of three palm tree peroxidases expressed by Escherichia coli: Uniqueness of African oil palm peroxidase

Palm tree peroxidase has greater catalytic activity, stability and broad application prospects in comparison with horseradish peroxidase. However, slow growth, ecological destruction and high costs prohibit isolation of native peroxidases directly from palm trees. Bioreactor production of palm tree peroxidases would therefore be preferred to overcome such production limitations. Comparison of different recombinant glycan-free palm tree peroxidases would allow understanding the criticality of total glycans to the functions and characteristics. In the present study, African oil palm tree peroxidase expressed by Escherichia coli showed similar stability and 30-100-fold greater activity than that of recombinant royal palm tree peroxidases, but both of their comprehensive indexes were superior to the commercial, native horseradish peroxidase. Recombinant Chamaerops excelsa peroxidase showed no activity possibly due to incorrect protein folding. The results confirmed that recombinant expression by E. coli is potentially an effective means to obtain a mass of palm peroxidases with high activity and stability.

An efficient methodology for the purification of date palm peroxidase: Stability comparison with horseradish peroxidase (HRP)

In the present study, Peroxidase from date palm (Phoenix dactylifera) leaves was purified to homogeneity by three-step procedure including aqueous two-phase system, hydrophobic and Ion-exchange chromatography. The enzyme migrated as single band on SDS-PAGE giving molecular weight of 68 ± 3 kDa. The purification factor for purified date palm peroxidase was 68 with high 41% yield. Enzymatic assays together with far-UV circular dichroism (CD), intrinsic and extrinsic fluorescence studies were carried out to monitor the structural stability of date palm and horseradish peroxidase (HRP) against various pH and temperatures. Activity measurements illustrated different pH stability for date palm and HRP. Both peroxidases are more susceptible to extreme acidic conditions as suggested by 4 & 15 nm red shift in date palm and HRP, respectively. Secondary structure analysis using far UV-CD exhibited predominance of α-helical (43.8%) structure. Also, pH induces loss in the secondary structure of date palm peroxidase. Thermal stability analysis revealed date palm peroxidase is more stable in comparison to HRP. In summary, date palm peroxidases could be promising enzymes for various applications where extreme pH and temperature is required.

Effect of N-Linked Glycosylation of Recombinant Windmill Palm Tree Peroxidase on Its Activity and Stability

Plant secretory peroxidases are valuable commercial enzymes. The windmill palm tree Trachycarpus fortunei produces one of the most stable and fastest peroxidases (WPTP) characterized to date; however, an economical source is needed. Pichia pastoris has been used as an expression system for WPTP and other peroxidases. However, yeast and plants synthesize different types of N-linked glycan structures and may differ the level of glycosylation at each site. Such non-native glycosylation can have unwanted consequences. Glycosylation site N256 was under-glycosylated in the wild-type (1.5%) compared to the native enzyme (55%); therefore, we mutated WPTP to promote glycosylation at this site (WPTP E254G). Glycosylation increased four-fold, as measured by liquid chromatography-tandem mass spectrometry. The mutation did not change the substrate specificity and optimal pH- and thermo-stability ranges, but it increased the catalytic activity 2-3-fold. In comparison with wild-type WPTP, WPTP E254G showed a shift of the most stable pH from 7 to 9, making it suitable for applications under alkaline conditions.

Characterization of the second conserved domain in the heme uptake protein HtaA from Corynebacterium diphtheriae

HtaA is a heme-binding protein that is part of the heme uptake system in Corynebacterium diphtheriae. HtaA contains two conserved regions (CR1 and CR2). It has been previously reported that both domains can bind heme; the CR2 domain binds hemoglobin more strongly than the CR1 domain. In this study, we report the biophysical characteristics of HtaA-CR2. UV-visible spectroscopy and resonance Raman experiments are consistent with this domain containing a single heme that is bound to the protein through an axial tyrosine ligand. Mutants of conserved tyrosine and histidine residues (Y361, H412, and Y490) have been studied. These mutants are isolated with very little heme (≤5%) in comparison to the wild-type protein (~20%). Reconstitution after removal of the heme with butanone gave an alternative form of the protein. The HtaA-CR2 fold is very stable; it was necessary to perform thermal denaturation experiments in the presence of guanidinium hydrochloride. HtaA-CR2 unfolds extremely slowly; even in 6.8M GdnHCl at 37°C, the half-life was 5h. In contrast, the apo forms of WT HtaA-CR2 and the aforementioned mutants unfolded at much lower concentrations of GdnHCl, indicating the role of heme in stabilizing the structure and implying that heme transfer is effected only to a partner protein in vivo.

Effects of clove essential oil and eugenol on quality and browning control of fresh-cut lettuce

This study confirmed the inhibitory effects of clove essential oil (CEO) and eugenol (EUG) on the browning and relevant enzymes of fresh-cut lettuce, and examined associated mechanisms by inhibition kinetics and computational docking analysis. Fresh-cut lettuce was treated with 0.05% CEO and 0.05% EUG solutions, resulting in inhibition of the deterioration of texture quality and browning of the lettuce surface and interior. Compared with the controls, CEO and EUG significantly inhibited the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), and peroxidase (POD, all p<0.05). EUG suppressed PAL, PPO, and POD in vitro in a dose-dependent manner, with IC50 values of 5.4±0.9, 29.5±3.5, and 61.9±6.7mM, respectively. The binding and inhibition effects of EUG on PAL, PPO, and POD, determined by inhibition kinetics and computational docking analysis, established EUG as a competitive inhibitor of these browning-relevant enzymes.

Kinetics of Spanish broom peroxidase obeys a Ping-Pong Bi-Bi mechanism with competitive inhibition by substrates

In plants, adverse conditions often induce an increase in reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). H2O2 is reduced to water, and thus becomes detoxified by enzymes such as Cytisus multiflorus peroxidase (CMP). Here, the steady-state kinetics of the H2O2-supported oxidation of different organic substrates by CMP was investigated. Analysis of the initial rates vs. H2O2 and reducing substrate concentrations proved to be consistent with a substrate-inhibited Ping-Pong Bi-Bi reaction mechanism. The phenomenological approach expresses the peroxidase Ping-Pong mechanism in the form of the Michaelis-Menten equation and affords an interpretation of the effects in terms of the kinetic parameters [Formula: see text] , [Formula: see text] , kcat, [Formula: see text] , [Formula: see text] and of the microscopic rate constants, k1 and k3, of the shared three-step catalytic cycle of peroxidases.