Characterization of Class III Peroxidases from Switchgrass

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Recent Progress on Peroxidase Modification and Application

Peroxdiase is one of the member of oxireductase super family, which has a broad substrate range and a variety of reaction types, including hydroxylation, epoxidation or halogenation of unactivated C-H bonds, and aromatic group or biophenol compounds. Here, we summarized the recently discovered enzymes with peroxidation activity, and focused on the special structures, sites, and corresponding strategies that can change the peroxidase catalytic activity, stability, and substrate range. The comparison of the structural differences between these natural enzymes and the mimic enzymes of binding nanomaterials and polymer materials is helpful to expand the application of peroxidase in industry. In addition, we also reviewed the catalytic application of peroxidase in the synthesis of important organic molecules and the degradation of pollutants.

Impact of Climate Change on Altered Fruit Quality with Organoleptic, Health Benefit, and Nutritional Attributes

As a consequence of global climate change, acute water deficit conditions, soil salinity, and high temperature have been on the rise in their magnitude and frequency, which have been found to impact plant growth and development negatively. However, recent evidence suggests that many fruit plants that face moderate abiotic stresses can result in beneficial effects on the postharvest storage characters of the fruits. Salinity, drought, and high temperature conditions stimulate the synthesis of abscisic acid (ABA), and secondary metabolites, which are vital for fruit quality. The secondary metabolites like phenolic acids and anthocyanins that accumulate under abiotic stress conditions have antioxidant activity, and therefore, such fruits have health benefits too. It has been noticed that fruits accumulate more sugar and anthocyanins owing to upregulation of phenylpropanoid pathway enzymes. The novel information that has been generated thus far indicates that the growth environment during fruit development influences the quality components of the fruits. But the quality depends on the trade-offs between productivity, plant defense, and the frequency, duration, and intensity of stress. In this review, we capture the current knowledge of the irrigation practices for optimizing fruit production in arid and semiarid regions and enhancement in the quality of fruit with the application of exogenous ABA and identify gaps that exist in our understanding of fruit quality under abiotic stress conditions.

Sesame (Sesamum indicum L.) response to drought stress: susceptible and tolerant genotypes exhibit different physiological, biochemical, and molecular response patterns

Drought is one of the main environmental stresses affecting the quality and quantity of sesame production worldwide. The present study was conducted to investigate the effect of drought stress and subsequent re-watering on physiological, biochemical, and molecular responses of two contrasted sesame genotypes (susceptible vs. tolerant). Results showed that plant growth, photosynthetic rate, stomatal conductance, transpiration rate, and relative water content were negatively affected in both genotypes during water deficit. Both genotypes accumulated more soluble sugars, free amino acids, and proline and exhibited an increased enzyme activity for peroxidase, catalase, superoxide dismutase, and pyruvate dehydrogenase in response to drought damages including increased lipid peroxidation and membrane disruption. However, the tolerant genotype revealed a more extended root system and a more efficient photosynthetic apparatus. It also accumulated more soluble sugars (152%), free amino acids (48%), proline (75%), and antioxidant enzymes while showing lower electrolyte leakage (26%), lipid peroxidation (31%), and starch (35%) content, compared to the susceptible genotype at severe drought. Moreover, drought-related genes such as MnSOD1, MnSOD2, and PDHA-M were more expressed in the tolerant genotype, which encode manganese-dependent superoxide dismutase and the alpha subunit of pyruvate dehydrogenase, respectively. Upon re-watering, tolerant genotype recovered to almost normal levels of photosynthesis, carboxylation efficiency, lipid peroxidation, and electrolyte leakage, while susceptible genotype still suffered critical issues. Overall, these results suggest that a developed root system and an efficient photosynthetic apparatus along with the timely and effective accumulation of protective compounds enabled the tolerant sesame to withstand stress and successfully return to a normal growth state after drought relief. The findings of this study can be used as promising criteria for evaluating genotypes under drought stress in future sesame breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01372-y.

ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses

Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H₂O₂) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as "gate keepers" by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.

A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids

In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress.

Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids

APX is a key antioxidant enzyme in higher plants, scavenging H2O2 with ascorbate in several cellular compartments. Here, we report the crystal structures of cytosolic ascorbate peroxidase from switchgrass (Panicum virgatum L., Pvi), a strategic feedstock plant with several end uses. The overall structure of PviAPX was similar to the structures of other APX family members, with a bound ascorbate molecule at the ɣ-heme edge pocket as in other APXs. Our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Significantly, our study suggested that PviAPX can oxidize a broad range of phenylpropanoids with δ-meso site in a rather similar efficiency, which reflects its role in the fortification of cell walls in response to insect feeding. Based on detailed structural and kinetic analyses and molecular docking, as well as that of closely related APX enzymes, the critical residues in each substrate-binding site of PviAPX are proposed. Taken together, these observations shed new light on the function and catalysis of PviAPX, and potentially benefit efforts improve plant health and biomass quality in bioenergy and forage crops.

Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum

The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.

Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition

Plant NADPH-dependent cytochrome P450 reductase (CPR) is a multidomain enzyme that donates electrons for hydroxylation reactions catalyzed by class II cytochrome P450 monooxygenases involved in the synthesis of many primary and secondary metabolites. These P450 enzymes include trans-cinnamate-4-hydroxylase, p-coumarate-3′-hydroxylase, and ferulate-5-hydroxylase involved in monolignol biosynthesis. Because of its role in monolignol biosynthesis, alterations in CPR activity could change the composition and overall output of lignin. Therefore, to understand the structure and function of three CPR subunits from sorghum, recombinant subunits SbCPR2a, SbCPR2b, and SbCPR2c were subjected to X-ray crystallography and kinetic assays. Steady-state kinetic analyses demonstrated that all three CPR subunits supported the oxidation reactions catalyzed by SbC4H1 (CYP73A33) and SbC3′H (CYP98A1). Furthermore, comparing the SbCPR2b structure with the well-investigated CPRs from mammals enabled us to identify critical residues of functional importance and suggested that the plant flavin mononucleotide–binding domain might be more flexible than mammalian homologs. In addition, the elucidated structure of SbCPR2b included the first observation of NADP⁺ in a native CPR. Overall, we conclude that the connecting domain of SbCPR2, especially its hinge region, could serve as a target to alter biomass composition in bioenergy and forage sorghums through protein engineering.

Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture

Demands for peroxidases (POX)s with diverse physicochemical properties have steadily grown as more applications of POXs are demonstrated. Plants are among the best sources of versatile POXs, and plant biotechnology, as an agricultural hassle-free technology, promises to circumvent the limitations of natural resource exploitation and to address the demands. Following this trend, it was shown that POX production steadily increased during the 31-day subculture of Alkanna frigida (from Boraginaceae) callus on Murashige-Skoog medium containing 2,4-dichlorophenoxyacetic acid (10^-6 M) and kinetin (10^-5 M). The purified cationic enzyme (POX_alf) maintained its optimal activity over pH 4-7 for 2 years. It was resistant to H₂O₂ high concentrations (IC50 = 543.7 mM) and showed high specific activity in the reaction with phenol (4320.5 AU mg^-1 > 20-fold of HRP AU). Furthermore, the specificity constant ratio of guaiacol to phenol indicated a 100 times faster reaction of POX_alf with guaiacol. However, in contrast to HRP, it had little effect on diazo derivatives of aniline and meta-diaminobenzene. Based on the resulting primary structure from the tandem mass analysis, the POX_alf 3D structure was constructed via homology modelling. Despite the high topological similarity between the HRP and POX_alf structures, there were important differences between the active site pockets that could explain the observed differences in the corresponding substrate spectra and the specific activities. Considering the dynamics of POX_alf production, its inactivity towards IAA and its high affinity for guaiacol, POX_alf may have associated roles with A. frigida cell wall construction and monolignol metabolism.

The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato

Soil salinity and drought limit sweet potato yield. Scavenging of reactive oxygen species (ROS) by peroxidases (PRXs) is essential during plant stress responses, but how PRX expression is regulated under abiotic stress is not well understood. Here, we report that the B-box (BBX) family transcription factor IbBBX24 activates the expression of the class III peroxidase gene IbPRX17 by binding to its promoter. Overexpression of IbBBX24 and IbPRX17 significantly improved the tolerance of sweet potato to salt and drought stresses, whereas reducing IbBBX24 expression increased their susceptibility. Under abiotic stress, IbBBX24- and IbPRX17-overexpression lines showed higher peroxidase activity and lower H₂ O₂ accumulation compared with the wild-type. RNA sequencing analysis revealed that IbBBX24 modulates the expression of genes encoding ROS scavenging enzymes, including PRXs. Moreover, interaction between IbBBX24 and the APETALA2 (AP2) protein IbTOE3 enhances the ability of IbBBX24 to activate IbPRX17 transcription. Overexpression of IbTOE3 improved the tolerance of tobacco plants to salt and drought stresses by scavenging ROS. Together, our findings elucidate the mechanism underlying the IbBBX24-IbTOE3-IbPRX17 module in response to abiotic stress in sweet potato and identify candidate genes for developing elite crop varieties with enhanced abiotic stress tolerance.

Signatures of selection in recently domesticated macadamia

Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar ‘Kau’ and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for ‘one-step operation’ for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.

Macadamia is a recently domesticated nut crop. Here, the authors report the genome assembly of Hawaiian cultivar ‘Kau’ and conduct population genomic analyses to reveal the origin of Hawaiian cultivars and the genomic basis for one-step operation for the clonal crop domestication.

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.

Evolutionary Implications of a Peroxidase with High Affinity for Cinnamyl Alcohols from Physcomitrium patens, a Non-Vascular Plant

Physcomitrium (Physcomitrella) patens is a bryophyte highly tolerant to different stresses, allowing survival when water supply is a limiting factor. This moss lacks a true vascular system, but it has evolved a primitive water-conducting system that contains lignin-like polyphenols. By means of a three-step protocol, including ammonium sulfate precipitation, adsorption chromatography on phenyl Sepharose and cationic exchange chromatography on SP Sepharose, we were able to purify and further characterize a novel class III peroxidase, PpaPrx19, upregulated upon salt and H₂O₂ treatments. This peroxidase, of a strongly basic nature, shows surprising homology to angiosperm peroxidases related to lignification, despite the lack of true lignins in P. patens cell walls. Moreover, PpaPrx19 shows catalytic and kinetic properties typical of angiosperm peroxidases involved in oxidation of monolignols, being able to efficiently use hydroxycinnamyl alcohols as substrates. Our results pinpoint the presence in P. patens of peroxidases that fulfill the requirements to be involved in the last step of lignin biosynthesis, predating the appearance of true lignin.

Recombinant Expression and Characterization of Lemon (Citrus limon) Peroxidase

BACKGROUND

Class III plant peroxidases play important role in a number of physiological processes in plants such as lignin biosynthesis, suberization, cell wall biosynthesis, reactive oxygen species metabolism and plant defense against pathogens. Peroxidases are also of significance in several industrial applications. In view of this, the production and identification of novel peroxidases having resistance towards temperature, pH, salts is desirable.

OBJECTIVE

The objective of the present work was to clone and characterize a novel plant peroxidase suitable for industrial application.

METHODS

A full length cDNA clone of lemon peroxidase was isolated using PCR and RACE approaches, characterized and heterologously expressed in Escherichia coli using standard protocols. The expressed peroxidase was purified using Ni-NTA agarose column and biochemically characterized using standard protocols. The peroxidase was also in-silico characterized at nucleotide as well as protein levels using standard protocols.

RESULTS

A full length cDNA clone of lemon peroxidase was isolated and expressed heterologously in E. coli. The expressed recombinant lemon peroxidase (LPRX) was activated by in-vitro refolding and purified. The purified LPRX exhibited pH and temperature optima of pH 7.0 and 50°C, respectively. The LPRX was found to be activated by metal ions (Na+, Ca2+, Mg2+ and Mn2+) at lower concentration. The expressional analysis of the transcripts suggested involvement of lemon peroxidase in plant defense. The lemon peroxidase was in silico modelled and docked with the substrates guaiacol, and pyrogallol and shown the favourability of pyrogallol over guaiacol, which is in agreement with the in-vitro findings. The protein function annotation analyses suggested the involvement of lemon peroxidase in the phenylpropanoid biosynthesis pathway and plant defense mechanisms.

CONCLUSION

Based on the biochemical characterization, the purified peroxidase was found to be resistant towards the salts and thus, might be a good candidate for industrial exploitation. The in-silico protein function annotation and transcript analyses highlighted the possible involvement of the lemon peroxidase in plant defense response.

Genome-wide identification and analysis of class III peroxidases in Betula pendula

BACKGROUND

Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula.

RESULTS

We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times.

CONCLUSIONS

The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

Structure and Function of the Cytochrome P450 Monooxygenase Cinnamate 4-hydroxylase from Sorghum bicolor

Cinnamate 4-hydroxylase (C4H; CYP73A) is a cytochrome P450 monooxygenase associated externally with the endoplasmic reticulum of plant cells. The enzyme uses NADPH-cytochrome P450 reductase as a donor of electrons and hydroxylates cinnamic acid to form 4-coumaric acid in phenylpropanoid metabolism. In order to better understand the structure and function of this unique class of plant P450 enzymes, we have characterized the enzyme C4H1 from lignifying tissues of sorghum (Sorghum bicolor), encoded by Sobic.002G126600 Here we report the 1.7 Å resolution crystal structure of CYP73A33. The obtained structural information, along with the results of the steady-state kinetic analysis and the absorption spectroscopy titration, displays a high degree of similarity of the structural and functional features of C4H to those of other P450 proteins. Our data also suggest the presence of a putative allosteric substrate-binding site in a hydrophobic pocket on the enzyme surface. In addition, comparing the newly resolved structure with those of well-investigated cytochromes P450 from mammals and bacteria enabled us to identify those residues of critical functional importance and revealed a unique sequence signature that is potentially responsible for substrate specificity and catalytic selectivity of C4H.

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

BACKGROUND

The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

RESULTS

We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

CONCLUSIONS

In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

Cellular and Genetic Regulation of Coniferaldehyde Incorporation in Lignin of Herbaceous and Woody Plants by Quantitative Wiesner Staining

Lignin accumulates in the cell walls of specialized cell types to enable plants to stand upright and conduct water and minerals, withstand abiotic stresses, and defend themselves against pathogens. These functions depend on specific lignin concentrations and subunit composition in different cell types and cell wall layers. However, the mechanisms controlling the accumulation of specific lignin subunits, such as coniferaldehyde, during the development of these different cell types are still poorly understood. We herein validated the Wiesner test (phloroglucinol/HCl) for the restrictive quantitative in situ analysis of coniferaldehyde incorporation in lignin. Using this optimized tool, we investigated the genetic control of coniferaldehyde incorporation in the different cell types of genetically-engineered herbaceous and woody plants with modified lignin content and/or composition. Our results demonstrate that the incorporation of coniferaldehyde in lignified cells is controlled by (a) autonomous biosynthetic routes for each cell type, combined with (b) distinct cell-to-cell cooperation between specific cell types, and (c) cell wall layer-specific accumulation capacity. This process tightly regulates coniferaldehyde residue accumulation in specific cell types to adapt their property and/or function to developmental and/or environmental changes.

Phenolic cross-links: building and de-constructing the plant cell wall

Covering: Up to 2019Phenolic cross-links and phenolic inter-unit linkages result from the oxidative coupling of two hydroxycinnamates or two molecules of tyrosine. Free dimers of hydroxycinnamates, lignans, play important roles in plant defence. Cross-linking of bound phenolics in the plant cell wall affects cell expansion, wall strength, digestibility, degradability, and pathogen resistance. Cross-links mediated by phenolic substituents are particularly important as they confer strength to the wall via the formation of new covalent bonds, and by excluding water from it. Four biopolymer classes are known to be involved in the formation of phenolic cross-links: lignins, extensins, glucuronoarabinoxylans, and side-chains of rhamnogalacturonan-I. Lignins and extensins are ubiquitous in streptophytes whereas aromatic substituents on xylan and pectic side-chains are commonly assumed to be particular features of Poales sensu lato and core Caryophyllales, respectively. Cross-linking of phenolic moieties proceeds via radical formation, is catalyzed by peroxidases and laccases, and involves monolignols, tyrosine in extensins, and ferulate esters on xylan and pectin. Ferulate substituents, on xylan in particular, are thought to be nucleation points for lignin polymerization and are, therefore, of paramount importance to wall architecture in grasses and for the development of technology for wall disassembly, e.g. for the use of grass biomass for production of 2^nd generation biofuels. This review summarizes current knowledge on the intra- and extracellular acylation of polysaccharides, and inter- and intra-molecular cross-linking of different constituents. Enzyme mediated lignan in vitro synthesis for pharmaceutical uses are covered as are industrial exploitation of mutant and transgenic approaches to control cell wall cross-linking.

The Significance of Reactive Oxygen Species and Antioxidant Defense System in Plants: A Concise Overview

In plants, there is a complex and multilevel network of the antioxidative system (AOS) operating to counteract harmful reactive species (RS), the foremost important of which are reactive oxygen species (ROS), and maintain homeostasis within the cell. Specific AOSs for plant cells are, first and foremost, enzymes of the glutathione-ascorbate cycle (Asc-GSH), followed by phenolic compounds and lipophilic antioxidants like carotenoids and tocopherols. Evidence that plant cells have excellent antioxidative defense systems is their ability to survive at H₂O₂ concentrations incompatible with animal cell life. For the survival of stressed plants, it is of particular importance that AOS cooperate and participate in redox reactions, therefore, providing better protection and regeneration of the active reduced forms. Considering that plants abound in antioxidant compounds, and humans are not predisposed to synthesize the majority of them, new fields of research have emerged. Antioxidant potential of plant compounds has been exploited for anti-aging formulations preparation, food fortification and preservation but also in designing new therapies for diseases with oxidative stress implicated in etiology.

In Silico Analysis of Class III Peroxidases: Hypothetical Structure, Ligand Binding Sites, Posttranslational Modifications, and Interaction with Substrates

Functional analyses of peroxidases are a major challenge. In silico analysis appears to be a powerful tool to overcome at least some of the problems that arose from (1) the numerous possible functions of peroxidases, (2) their low substrate specificity, and (3) the compensation of knockout mutants by other isoenzymes. Amino acid sequences and crystal structures of peroxidases were used for the prediction of tertiary structures, posttranslational modifications, ligand and substrate binding sites, and so on of uncharacterized peroxidases. This protocol presents tools and their applications for an in silico analysis of soluble and membrane-bound peroxidases, but it may be used for other proteins, too.

Designing a cocktail containing redox enzymes to improve hemicellulosic hydrolysate fermentability by microorganisms

Bioproducts production using monomeric sugars derived from lignocellulosic biomass presents several challenges, such as to require a physicochemical pretreatment to improve its conversion yields. Hydrothermal lignocellulose pretreatment has several advantages and results in solid and liquid streams. The former is called hemicellulosic hydrolysate (HH), which contains inhibitory phenolic compounds and sugar degradation products that hinder microbial fermentation products from pentose sugars. Here, we developed and applied a novel enzyme process to detoxify HH. Initially, the design of experiments with different redox activities enzymes was carried out. The enzyme mixture containing the peroxidase (from Armoracia rusticana) together with superoxide dismutase (from Coptotermes gestroi) are the most effective to detoxify HH derived from sugarcane bagasse. Butanol fermentation by the bacteria Clostridium saccharoperbutylacetonicum and ethanol production by the yeast Scheffersomyces stipitis increased by 24.0× and 2.4×, respectively, relative to the untreated hemicellulosic hydrolysates. Detoxified HH was analyzed by chromatographic and spectrometric methods elucidating the mechanisms of phenolic compound modifications by enzymatic treatment. The enzyme mixture degraded and reduced the hydroxyphenyl- and feruloyl-derived units and polymerized the lignin fragments. This strategy uses biocatalysts under environmentally friendly conditions and could be applied in the fuel, food, and chemical industries.

Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

Orchestration of Cu-Zn SOD and class III peroxidase with upstream interplay between NADPH oxidase and PM H+-ATPase mediates root growth in Vigna radiata (L.) Wilczek

Post-germination plant growth depends on the regulation of reactive oxygen species (ROS) metabolism, spatiotemporal pH changes and Ca⁺² homeostasis, whose potential integration has been studied during Vigna radiata (L.) Wilczek root growth. The dissipation of proton (H⁺) gradients across plasma membrane (PM) by CCCP (protonophore) and the inhibition of PM H⁺-ATPase by sodium orthovanadate repressed SOD (superoxide dismutase; EC 1.15.1.1) activity as revealed by spectrophotometric and native PAGE assay results. Similar results derived from treatment with DPI (NADPH oxidase inhibitor) and Tiron (O₂- scavenger) denote a functional synchronization of SOD, PM H⁺-ATPase and NOX, as the latter two enzymes are substrate sources for SOD (H⁺ and O₂-, respectively) and are involved in a feed-forward loop. After SOD inactivation, a decline in apoplastic H₂O₂ content was observed in each treatment group, emerging as a possible cause of the diminution of class III peroxidase (Prx; EC 1.11.1.7), which utilizes H₂O₂ as a substrate. In agreement with the pivotal role of Ca⁺² in PM H⁺-ATPase and NOX activation, Ca⁺² homeostasis antagonists, i.e., LaCl₃ (Ca⁺² channel inhibitor), EGTA (Ca⁺² chelator) and LiCl (endosomal Ca⁺² release blocker), inhibited both SOD and Prx. Finally, a drastic reduction in apoplastic OH (hydroxyl radical) concentrations (induced by each treatment, leading to Prx inhibition) was observed via fluorometric analysis. A consequential inhibition of root growth observed under each treatment denotes the importance of the orchestrated functioning of PM H⁺-ATPase, NOX, Cu-Zn SOD and Prx during root growth. A working model demonstrating postulated enzymatic synchronization with an intervening role of Ca⁺² is proposed.

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions

Class III peroxidases are heme-containing proteins of the secretory pathway with a high redundance and versatile functions. Many soluble peroxidases have been characterized in great detail, whereas only a few studies exist on membrane-bound isoenzymes. Membrane localization of class III peroxidases has been demonstrated for tonoplast, plasma membrane and detergent resistant membrane fractions of different plant species. In silico analysis revealed transmembrane domains for about half of the class III peroxidases that are encoded by the maize (Zea mays) genome. Similar results have been found for other species like thale-cress (Arabidopsis thaliana), barrel medic (Medicago truncatula) and rice (Oryza sativa). Besides this, soluble peroxidases interact with tonoplast and plasma membranes by protein⁻protein interaction. The topology, spatiotemporal organization, molecular and biological functions of membrane-bound class III peroxidases are discussed. Besides a function in membrane protection and/or membrane repair, additional functions have been supported by experimental data and phylogenetics.

Biochemical and Structural Analysis of Substrate Specificity of a Phenylalanine Ammonia-Lyase

Phenylalanine ammonia-lyase (PAL) is the first enzyme of the general phenylpropanoid pathway catalyzing the nonoxidative elimination of ammonia from l-phenylalanine to give trans-cinnamate. In monocots, PAL also displays tyrosine ammonia lyase (TAL) activity, leading to the formation of p-coumaric acid. The catalytic mechanism and substrate specificity of a major PAL from sorghum (Sorghum bicolor; SbPAL1), a strategic plant for bioenergy production, were deduced from crystal structures, molecular docking, site-directed mutagenesis, and kinetic and thermodynamic analyses. This first crystal structure of a monocotyledonous PAL displayed a unique conformation in its flexible inner loop of the 4-methylidene-imidazole-5-one (MIO) domain compared with that of dicotyledonous plants. The side chain of histidine-123 in the MIO domain dictated the distance between the catalytic MIO prosthetic group created from ¹⁸⁹Ala-Ser-Gly¹⁹¹ residues and the bound l-phenylalanine and l-tyrosine, conferring the deamination reaction through either the Friedel-Crafts or E₂ reaction mechanism. Several recombinant mutant SbPAL1 enzymes were generated via structure-guided mutagenesis, one of which, H123F-SbPAL1, has 6.2 times greater PAL activity without significant TAL activity. Additional PAL isozymes of sorghum were characterized and categorized into three groups. Taken together, this approach identified critical residues and explained substrate preferences among PAL isozymes in sorghum and other monocots, which can serve as the basis for the engineering of plants with enhanced biomass conversion properties, disease resistance, or nutritional quality.

The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD4

Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis, reducing sinapaldehyde, coniferaldehyde, and p-coumaraldehyde to their corresponding alcohols in an NADPH-dependent manner. Because of its terminal location in monolignol biosynthesis, the variation in substrate specificity and activity of CAD can result in significant changes in overall composition and amount of lignin. Our in-depth characterization of two major CAD isoforms, SbCAD2 (Brown midrib 6 [bmr6]) and SbCAD4, in lignifying tissues of sorghum (Sorghum bicolor), a strategic plant for generating renewable chemicals and fuels, indicates their similarity in both structure and activity to Arabidopsis (Arabidopsis thaliana) CAD5 and Populus tremuloides sinapyl alcohol dehydrogenase, respectively. This first crystal structure of a monocot CAD combined with enzyme kinetic data and a catalytic model supported by site-directed mutagenesis allows full comparison with dicot CADs and elucidates the potential signature sequence for their substrate specificity and activity. The L119W/G301F-SbCAD4 double mutant displayed its substrate preference in the order coniferaldehyde > p-coumaraldehyde > sinapaldehyde, with higher catalytic efficiency than that of both wild-type SbCAD4 and SbCAD2. As SbCAD4 is the only major CAD isoform in bmr6 mutants, replacing SbCAD4 with L119W/G301F-SbCAD4 in bmr6 plants could produce a phenotype that is more amenable to biomass processing.