Putative cationic cell-wall-bound peroxidase homologues in Arabidopsis, AtPrx2, AtPrx25, and AtPrx71, are involved in lignification

VAMP726 from maize and Arabidopsis confers pollen resistance to heat and UV radiation by influencing lignin content of sporopollenin

Sporopollenin in the pollen cell wall protects male gametophytes from stresses. Phenylpropanoid derivatives, including guaiacyl (G) lignin units, are known to be structural components of sporopollenin, but the exact composition of sporopollenin remains to be fully resolved. We analyzed the phenylpropanoid derivatives in sporopollenin from maize and Arabidopsis by thioacidolysis coupled with nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS). The NMR and GC-MS results confirmed the presence of p-hydroxyphenyl (H), G, and syringyl (S) lignin units in sporopollenin from maize and Arabidopsis. Strikingly, H units account for the majority of lignin monomers in sporopollenin from these species. We next performed a genome-wide association study to explore the genetic basis of maize sporopollenin composition and identified a vesicle-associated membrane protein (ZmVAMP726) that is strongly associated with lignin monomer composition of maize sporopollenin. Genetic manipulation of VAMP726 affected not only lignin monomer composition in sporopollenin but also pollen resistance to heat and UV radiation in maize and Arabidopsis, indicating that VAMP726 is functionally conserved in monocot and dicot plants. Our work provides new insight into the lignin monomers that serve as structural components of sporopollenin and characterizes VAMP726, which affects sporopollenin composition and stress resistance in pollen.

Comparative transcriptome analysis reveals key pathways and genes involved in trichome development in tea plant (Camellia sinensis)

Trichomes, which develop from epidermal cells, are considered one of the important characteristics of the tea plant [Camellia sinensis (L.) O. Kuntze]. Many nutritional and metabolomic studies have indicated the important contributions of trichomes to tea products quality. However, understanding the regulation of trichome formation at the molecular level remains elusive in tea plants. Herein, we present a genome-wide comparative transcriptome analysis between the hairless Chuyeqi (CYQ) with fewer trichomes and the hairy Budiaomao (BDM) with more trichomes tea plant genotypes, toward the identification of biological processes and functional gene activities that occur during trichome development. In the present study, trichomes in both cultivars CYQ and BDM were unicellular, unbranched, straight, and soft-structured. The density of trichomes was the highest in the bud and tender leaf periods. Further, using the high-throughput sequencing method, we identified 48,856 unigenes, of which 31,574 were differentially expressed. In an analysis of 208 differentially expressed genes (DEGs) encoding transcription factors (TFs), five may involve in trichome development. In addition, on the basis of the Gene Ontology (GO) annotation and the weighted gene co-expression network analysis (WGCNA) results, we screened several DEGs that may contribute to trichome growth, including 66 DEGs related to plant resistance genes (PRGs), 172 DEGs related to cell wall biosynthesis pathway, 29 DEGs related to cell cycle pathway, and 45 DEGs related to cytoskeleton biosynthesis. Collectively, this study provided high-quality RNA-seq information to improve our understanding of the molecular regulatory mechanism of trichome development and lay a foundation for additional trichome studies in tea plants.

Populus alba cationic cell-wall-bound peroxidase (CWPO-C) regulates the plant growth and affects auxin concentration in Arabidopsis thaliana

The poplar cationic cell-wall-bound peroxidase (CWPO-C) mediates the oxidative polymerization of lignin precursors, especially sinapyl alcohols, and high molecular weight compounds that cannot be oxidized by other plant peroxidases, including horseradish peroxidase C. Therefore, CWPO-C is believed to be a lignification-specific peroxidase, but direct evidence of its function is lacking. Thus, the CWPO-C expression pattern in Arabidopsis thaliana (Arabidopsis) was determined using the β-glucuronidase gene as a reporter. Our data indicated that CWPO-C  was expressed in young organs, including the meristem, leaf, root, flower, and young xylem in the upper part of the stem. Compared with the wild-type control, transgenic Arabidopsis plants overexpressing CWPO-C had shorter stems. Approximately 60% of the plants in the transgenic line with the highest CWPO-C content had curled stems. These results indicate that CWPO-C plays a role in cell elongation. When plants were placed horizontally, induced CWPO-C expression was detected in the curved part of the stem during the gravitropic response. The stem curvature associated with gravitropism is controlled by auxin localization. The time needed for Arabidopsis plants overexpressing CWPO-C placed horizontally to bend by 90° was almost double the time required for the similarly treated wild-type controls. Moreover, the auxin content was significantly lower in the CWPO-C-overexpressing plants than in the wild-type plants. These results strongly suggest that CWPO-C has pleiotropic effects on plant growth and indole-3-acetic acid (IAA) accumulation. These effects may be mediated by altered IAA concentration due to oxidation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01241-0.

PtomtAPX is an autonomous lignification peroxidase during the earliest stage of secondary wall formation in Populus tomentosa Carr

At present, a cooperative process hypothesis is used to explain the supply of enzyme (class III peroxidases and/or laccases) and substrates during lignin polymerization. However, it remains elusive how xylem cells meet the needs of early lignin rapid polymerization during secondary cell wall formation. Here we provide evidence that a mitochondrial ascorbate peroxidase (PtomtAPX) is responsible for autonomous lignification during the earliest stage of secondary cell wall formation in Populus tomentosa. PtomtAPX was relocated to cell walls undergoing programmed cell death and catalysed lignin polymerization in vitro. Aberrant phenotypes were caused by altered PtomtAPX expression levels in P. tomentosa. These results reveal that PtomtAPX is crucial for catalysing lignin polymerization during the early stages of secondary cell wall formation and xylem development, and describe how xylem cells provide autonomous enzymes needed for lignin polymerization during rapid formation of the secondary cell wall by coupling with the programmed cell death process.

Regulation of lignin biosynthesis by an atypical bHLH protein CmHLB in Chrysanthemum

Stem mechanical strength is one of the most important agronomic traits that affects the resistance of plants against insects and lodging, and plays an essential role in the quality and yield of plants. Several transcription factors regulate mechanical strength in crops. However, mechanisms of stem strength formation and regulation remain largely unexplored, especially in ornamental plants. In this study, we identified an atypical bHLH transcription factor CmHLB (HLH PROTEIN INVOLVED IN LIGNIN BIOSYNTHESIS) in chrysanthemum, belonging to a small bHLH sub-family - the PACLOBUTRAZOL RESISTANCE (PRE) family. Overexpression of CmHLB in chrysanthemum significantly increased mechanical strength of the stem, cell wall thickness, and lignin content, compared with the wild type. In contrast, CmHLB RNA interference lines exhibited the opposite phenotypes. RNA-seq analysis indicated that CmHLB promoted the expression of genes involved in lignin biosynthesis. Furthermore, we demonstrated that CmHLB interacted with Chrysanthemum KNOTTED ARABIDOPSIS THALIANA7 (CmKNAT7) through the KNOX2 domain, which has a conserved function, i.e. it negatively regulates secondary cell wall formation of fibres and lignin biosynthesis. Collectively, our results reveal a novel role for CmHLB in regulating lignin biosynthesis by interacting with CmKNAT7 and affecting stem mechanical strength in Chrysanthemum.

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.

De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots

Background

Panax notoginseng (Burk.) F. H. Chen (PN) belonging to the genus Panax of family Araliaceae is widely used in traditional Chinese medicine to treat various diseases. PN taproot, as the most vital organ for the accumulation of bioactive components, presents a variable morphology (oval or long), even within the same environment. However, no related studies have yet explained the molecular mechanism of phenotypic differences. To investigate the cause of differences in the taproot phenotype, de novo and comparative transcriptomic analysis on PN taproot was performed.

Results

A total of 133,730,886 and 114,761,595 paired-end clean reads were obtained based on high-throughput sequencing from oval and long taproot samples, respectively. 121,955 unigenes with contig N50 = 1,774 bp were generated by using the de novo assembly transcriptome, 63,133 annotations were obtained with the BLAST. And then, 42 genes belong to class III peroxidase (PRX) gene family, 8 genes belong to L-Ascorbate peroxidase (APX) gene family, and 55 genes belong to a series of mitogen-activated protein kinase (MAPK) gene family were identified based on integrated annotation results. Differentially expressed genes analysis indicated substantial up-regulation of PnAPX3 and PnPRX45, which are related to reactive oxygen species metabolism, and the PnMPK3 gene, which is related to cell proliferation and plant root development, in long taproots compared with that in oval taproots. Furthermore, the determination results of real-time quantitative PCR, enzyme activity, and H₂O₂ content verified transcriptomic analysis results.

Conclusion

These results collectively demonstrate that reactive oxygen species (ROS) metabolism and the PnMPK3 gene may play vital roles in regulating the taproot phenotype of PN. This study provides further insights into the genetic mechanisms of phenotypic differences in other species of the genus Panax.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08283-w.

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs' amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

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.

Genome-wide association studies reveal the coordinated regulatory networks underlying photosynthesis and wood formation in Populus

Photosynthesis and wood formation underlie the ability of trees to provide renewable resources and perform ecological functions; however, the genetic basis and regulatory pathways coordinating these two linked processes remain unclear. Here, we used a systems genetics strategy, integrating genome-wide association studies, transcriptomic analyses, and transgenic experiments, to investigate the genetic architecture of photosynthesis and wood properties among 435 unrelated individuals of Populus tomentosa, and unravel the coordinated regulatory networks resulting in two trait categories. We detected 222 significant single-nucleotide polymorphisms, annotated to 177 candidate genes, for 10 traits of photosynthesis and wood properties. Epistasis uncovered 74 epistatic interactions for phenotypes. Strikingly, we deciphered the coordinated regulation patterns of pleiotropic genes underlying phenotypic variations for two trait categories. Furthermore, expression quantitative trait nucleotide mapping and coexpression analysis were integrated to unravel the potential transcriptional regulatory networks of candidate genes coordinating photosynthesis and wood properties. Finally, heterologous expression of two pleiotropic genes, PtoMYB62 and PtoMYB80, in Arabidopsis thaliana demonstrated that they control regulatory networks balancing photosynthesis and stem secondary cell wall components, respectively. Our study provides insights into the regulatory mechanisms coordinating photosynthesis and wood formation in poplar, and should facilitate genetic breeding in trees via molecular design.

The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators

Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H⁺-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr³¹ phosphorylation site for growth regulation in the Arabidopsis root tip.

Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

Korla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.

Early transcriptome changes induced by the Geminivirus C4 oncoprotein: setting the stage for oncogenesis

BACKGROUND

The Beet curly top virus C4 oncoprotein is a pathogenic determinant capable of inducing extensive developmental abnormalities. No studies to date have investigated how the transcriptional profiles differ between plants expressing or not expressing the C4 oncoprotein.

RESULTS

We investigated early transcriptional changes in Arabidopsis associated with expression of the Beet curly top virus C4 protein that represent initial events in pathogenesis via a comparative transcriptional analysis of mRNAs and small RNAs. We identified 48 and 94 differentially expressed genes at 6- and 12-h post-induction versus control plants. These early time points were selected to focus on direct regulatory effects of C4 expression. Since previous evidence suggested that the C4 protein regulated the brassinosteroid (BR)-signaling pathway, differentially expressed genes could be divided into two groups: those responsive to alterations in the BR-signaling pathway and those uniquely responsive to C4. Early transcriptional changes that disrupted hormone homeostasis, 18 and 19 differentially expressed genes at both 6- and 12-hpi, respectively, were responsive to C4-induced regulation of the BR-signaling pathway. Other C4-induced differentially expressed genes appeared independent of the BR-signaling pathway at 12-hpi, including changes that could alter cell development (4 genes), cell wall homeostasis (5 genes), redox homeostasis (11 genes) and lipid transport (4 genes). Minimal effects were observed on expression of small RNAs.

CONCLUSION

This work identifies initial events in genetic regulation induced by a geminivirus C4 oncoprotein. We provide evidence suggesting the C4 protein regulates multiple regulatory pathways and provides valuable insights into the role of the C4 protein in regulating initial events in pathogenesis.

Magnetic Field Induced Changes in the Shoot and Root Proteome of Barley (Hordeum vulgare L.)

The geomagnetic field (GMF) has been present since the beginning of plant evolution. Recently, some researchers have focused their efforts on employing magnetic fields (MFs) higher than GMF to improve the seed germination, growth, and harvest of agriculturally important crop plants, as the use of MFs is an inexpensive and environment-friendly technique. In this study, we have employed different treatments of MF at 7 mT (milliTesla) at different time points of exposure, including 1, 3, and 6 h. The extended exposure was followed by five consecutive days at 6 h per day in barley seeds. The results showed a positive impact of MF on growth characteristics for 5-day-old seedlings, including seed germination rate, root and shoot length, and biomass weight. Furthermore, ~5 days of delay of flowering in pre-treated plants was also observed. We used a shotgun proteomics approach to identify changes in the protein signatures of root and shoot tissues under MF effects. In total, we have identified 2,896 proteins. Thirty-eight proteins in the shoot and 15 proteins in the root showed significant changes under the MF effect. Proteins involved in primary metabolic pathways were increased in contrast to proteins with a metal ion binding function, proteins that contain iron ions in their structure, and proteins involved in electron transfer chain, which were all decreased significantly in the treated tissues. The upregulated proteins' overall biological processes included carbohydrate metabolic process, oxidation-reduction process, and cell redox homeostasis, while down-regulated processes included translation and protein refolding. In general, shoot response was more affected by MF effect than root tissue, leading to the identification of 41 shoot specific proteins. This study provides an initial insight into the proteome regulation response to MF during barley's seedling stage.

High-order mutants reveal an essential requirement for peroxidases but not laccases in Casparian strip lignification

Lignin is a defining polymer of vascular plants and of great physiological, ecological, and economical importance. Yet, its polymerization in the cell wall is still not understood. Lignin polymerizing enzymes, laccases and peroxidases, exist in vast numbers in plant genomes. By focusing on a specific lignin structure, the ring-like Casparian strips (CSs), we reduced candidate numbers and abolished essentially all laccases with detectable endodermal expression. Yet, not even slight defects in CS formation were detected. By contrast, a quintuple peroxidase mutant displayed a complete absence of CS. Our findings suggest that cells lignify differently depending on whether lignin is localized or ubiquitous and whether cells stay alive during and after lignification, as well as the composition of the cell wall.

Lignin has enabled plants to colonize land, grow tall, transport water within their bodies, and protect themselves against various stresses. Consequently, this polyphenolic polymer, impregnating cellulosic plant cell walls, is the second most abundant polymer on Earth. Yet, despite its great physiological, ecological, and economical importance, our knowledge of lignin biosynthesis in vivo, especially the polymerization steps within the cell wall, remains vague—specifically, the respective roles of the two polymerizing enzymes classes, laccases and peroxidases. One reason for this lies in the very high numbers of laccases and peroxidases encoded by 17 and 73 homologous genes, respectively, in Arabidopsis. Here, we have focused on a specific lignin structure, the ring-like Casparian strips (CSs) within the root endodermis. By reducing candidate numbers using cellular resolution expression and localization data and by boosting stacking of mutants using CRISPR-Cas9, we mutated the majority of laccases in Arabidopsis in a nonuple mutant—essentially abolishing laccases with detectable endodermal expression. Yet, we were unable to detect even slight defects in CS formation. By contrast, we were able to induce a complete absence of CS formation in a quintuple peroxidase mutant. Our findings are in stark contrast to the strong requirement of xylem vessels for laccase action and indicate that lignin in different cell types can be polymerized in very distinct ways. We speculate that cells lignify differently depending on whether lignin is localized or ubiquitous and whether cells stay alive during and after lignification, as well as the composition of the cell wall.

Coordination of five class III peroxidase-encoding genes for early germination events of Arabidopsis thaliana

The Class III peroxidases (CIII Prxs) belong to a plant-specific multigene family. Thanks to their double catalytic cycle they can oxidize compounds or release reactive oxygen species (ROS). They are either involved in different cell wall stiffening processes such as lignification and suberization, in cell wall loosening or defense mechanisms. Germination is an important developmental stage requiring specific peroxidase activity. However, little is known about which isoforms are involved. Five CIII Prx encoding genes: AtPrx04, AtPrx16, AtPrx62, AtPrx69, and AtPrx71 were identified from published microarray data mining. Delayed or induced testa and endosperm rupture were observed for the corresponding CIII Prx mutant lines indicating either a gene-specific inducing or repressing role during germination, respectively. Via in situ hybridization AtPrx16, AtPrx62, AtPrx69 and AtPrx71 transcripts were exclusively localized to the micropylar endosperm facing the radicle, and transcriptomic data analysis enabled positioning the five CIII Prxs in a co-expression network enriched in germination, cell wall, cell wall proteins and xyloglucan hits. Evidence were produced showing that the five CIII Prxs were cell wall-targeted proteins and that the micropylar endosperm displayed a complex cell wall domain topochemistry. Finally, we drew a spatio-temporal model highlighting the fine sequential gene expression and the possible involvement of micropylar endosperm cell wall domains to explain the non-redundant cell wall stiffening and loosening functions of the CIII Prxs in a single cell type. We also highlighted the necessity of a peroxidase homeostasis to accurately control the micropylar endosperm cell wall dynamics during Arabidopsis germination events.

Grapevine VlbZIP30 improves drought resistance by directly activating VvNAC17 and promoting lignin biosynthesis through the regulation of three peroxidase genes

Drought stress severely affects grapevine quality and yield, and recent reports have revealed that lignin plays an important role in protection from drought stress. Since little is known about lignin-mediated drought resistance in grapevine, we investigated its significance. Herein, we show that VlbZIP30 mediates drought resistance by activating the expression of lignin biosynthetic genes and increasing lignin deposition. Transgenic grapevine plants overexpressing VlbZIP30 exhibited lignin deposition (mainly G and S monomers) in the stem secondary xylem under control conditions, which resulted from the upregulated expression of VvPRX4 and VvPRX72. Overexpression of VlbZIP30 improves drought tolerance, characterized by a reduction in the water loss rate, maintenance of an effective photosynthesis rate, and increased lignin content (mainly G monomer) in leaves under drought conditions. Electrophoretic mobility shift assay, luciferase reporter assays, and chromatin immunoprecipitation-qPCR assays indicated that VlbZIP30 directly binds to the G-box cis-element in the promoters of lignin biosynthetic (VvPRX N1) and drought-responsive (VvNAC17) genes to regulate their expression. In summary, we report a novel VlbZIP30-mediated mechanism linking lignification and drought tolerance in grapevine. The results of this study may be of value for the development of molecular breeding strategies to produce drought-resistant fruit crops.

UDP-GLYCOSYLTRANSFERASE 72E3 Plays a Role in Lignification of Secondary Cell Walls in Arabidopsis

Lignin is present in plant secondary cell walls and is among the most abundant biological polymers on Earth. In this work we investigated the potential role of the UGT72E gene family in regulating lignification in Arabidopsis. Chemical determination of floral stem lignin contents in ugt72e1, ugt72e2, and ugt72e3 mutants revealed no significant differences compared to WT plants. In contrast, the use of a novel safranin O ratiometric imaging technique indicated a significant increase in the cell wall lignin content of both interfascicular fibers and xylem from young regions of ugt72e3 mutant floral stems. These results were globally confirmed in interfascicular fibers by Raman microspectroscopy. Subsequent investigation using a bioorthogonal triple labelling strategy suggested that the augmentation in lignification was associated with an increased capacity of mutant cell walls to incorporate H-, G-, and S-monolignol reporters. Expression analysis showed that this increase was associated with an up-regulation of LAC17 and PRX71, which play a key role in lignin polymerization. Altogether, these results suggest that UGT72E3 can influence the kinetics of lignin deposition by regulating monolignol flow to the cell wall as well as the potential of this compartment to incorporate monomers into the growing lignin polymer.

The developmental dynamics of the sweet sorghum root transcriptome elucidate the differentiation of apoplastic barriers

Apoplastic barriers in the endodermis, such as Casparian strips and suberin lamellae, control the passage of water and minerals into the stele. Apoplastic barriers are thus thought to contribute to salt exclusion in salt-excluding plants such as sweet sorghum (Sorghum bicolor). However, little is known about the genes involved in the development of the apoplastic barrier. Here, we identified candidate genes involved in Casparian strip and suberin lamella development in the roots of a sweet sorghum line (M-81E). Three distinct developmental regions (no differentiation, developing, and mature) were identified based on Casparian strip and suberin lamella staining in root cross sections. Sequencing of RNA extracted from these distinct sections identified key genes participating in the differentiation of the apoplastic barrier. The different sections were structurally distinct, presumably due to differences in gene expression. Genes controlling the phenylpropanoid pathway, fatty acid elongation, and fatty acid ω-hydroxylation appeared to be directly responsible for the formation of the apoplastic barrier. Our dataset elucidates the molecular processes underpinning apoplastic barrier development and provides a basis for future research on molecular mechanisms of apoplastic barrier formation and salt exclusion.Abbreviations: SHR, SHORTROOT; MYB, MYB DOMAIN PROTEIN; CIFs, Casparian strip integrity factors; CASP, Casparian strip domain proteins; PER, peroxidase; ESB1, ENHANCED SUBERIN1; CS, Casparian strip; RPKM, reads per kilobase per million reads; DEGs, differentially expressed genes; FDR, false discovery rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; RNA-seq, RNA sequencing; PAL, phenylalanine ammonia-lyase; CYP, cytochrome P450 monooxygenases; 4CL, 4-coumarate-CoA ligase; AAE5, ACYL-ACTIVATING ENZYME5; CCR, cinnamoyl CoA reductase; TKPR, TETRAKETIDE ALPHA-PYRONE REDUCTASE1; CAD, cinnamyl alcohol dehydrogenase; HST, shikimate O-hydroxycinnamoyltransferase; PMAT2, PHENOLIC GLUCOSIDE MALONYLTRANSFERASE2; CCOAOMT, caffeoyl-CoA O-methyltransferase; KCS, β-ketoacyl-CoA synthase; CUT1, CUTICULAR PROTEIN1; DET2, 5-alpha-reductase; TAX, 3'-N-debenzoyl-2'-deoxytaxol N-benzoyltransferase; CER1, ECERIFERUM1; FAR, fatty acyl reductase; AF-CoA, alcohol-forming fatty acyl-CoA reductase; ABCG, ATP-binding cassette, subfamily G; ERF, ethylene-responsive transcription factor; HSF, heat stress transcription factor; NTF, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-5; GPAT, glycerol 3-phosphate acyltransferase.

Comparative Transcriptome Analysis Reveals Stem Secondary Growth of Grafted Rosa rugosa 'Rosea' Scion and R. multiflora 'Innermis' Rootstock

Grafted plant is a chimeric organism formed by the connection of scion and rootstock through stems, so stem growth and development become one of the important factors to affect grafted plant state. However, information regarding the molecular responses of stems secondary growth after grafting is limited. A grafted Rosa plant, with R. rugosa 'Rosea' as the scion (Rr_scion) grafted onto R. multiflora 'Innermis' as the stock (Rm_stock), has been shown to significantly improve stem thickness. To elucidate the molecular mechanisms of stem secondary growth in grafted plant, a genome-wide transcription analysis was performed using an RNA sequence (RNA-seq) method between the scion and rootstock. Comparing ungrafted R. rugosa 'Rosea' (Rr) and R. multiflora 'Innermis' (Rm) plants, there were much more differentially expressed genes (DEGs) identified in Rr_scion (6887) than Rm_stock (229). Functional annotations revealed that DEGs in Rr_scion are involved in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: the phenylpropanoid biosynthesis metabolism and plant hormone signal transduction, whereas DEGs in Rm_stock were associated with starch and sucrose metabolism pathway. Moreover, different kinds of signal transduction-related DEGs, e.g., receptor-like serine/threonine protein kinases (RLKs), transcription factor (TF), and transporters, were identified and could affect the stem secondary growth of both the scion and rootstock. This work provided new information regarding the underlying molecular mechanism between scion and rootstock after grafting.

PRX2 and PRX25, peroxidases regulated by COG1, are involved in seed longevity in Arabidopsis

Permeability is a crucial trait that affects seed longevity and is regulated by different polymers including proanthocyanidins, suberin, cutin and lignin located in the seed coat. By testing mutants in suberin transport and biosynthesis, we demonstrate the importance of this biopolymer to cope with seed deterioration. Transcriptomic analysis of cog1-2D, a gain-of-function mutant with increased seed longevity, revealed the upregulation of several peroxidase genes. Reverse genetics analysing seed longevity uncovered redundancy within the seed coat peroxidase gene family; however, after controlled deterioration treatment, seeds from the prx2 prx25 double and prx2 prx25 prx71 triple mutant plants presented lower germination than wild-type plants. Transmission electron microscopy analysis of the seed coat of these mutants showed a thinner palisade layer, but no changes were observed in proanthocyanidin accumulation or in the cuticle layer. Spectrophotometric quantification of acetyl bromide-soluble lignin components indicated changes in the amount of total polyphenolics derived from suberin and/or lignin in the mutant seeds. Finally, the increased seed coat permeability to tetrazolium salts observed in the prx2 prx25 and prx2 prx25 prx71 mutant lines suggested that the lower permeability of the seed coats caused by altered polyphenolics is likely to be the main reason explaining their reduced seed longevity.

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.

Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification

Five laccase genes are potentially involved in developmental lignification in the model C4 grass Setaria viridis and their different tissue specificities suggest subfunctionalization events. Plant laccases are copper-containing glycoproteins involved in monolignol oxidation and, therefore, their activity is essential for lignin polymerization. Although these enzymes belong to large multigene families with highly redundant members, not all of them are thought to be involved in lignin metabolism. Here, we report on the genome-wide characterization of the laccase gene family in the model C4 grass Setaria viridis and further identification of the members potentially involved in monolignol oxidation. A total of 52 genes encoding laccases (SvLAC1 to SvLAC52) were found in the genome of S. viridis, and phylogenetic analyses showed that these genes were heterogeneously distributed among the characteristic six subclades of the family and are under relaxed selective constraints. The observed expansion in the total number of genes in this species was mainly caused by tandem duplications within subclade V, which accounts for 68% of the whole family. Comparative phylogenetic analyses showed that the expansion of subclade V is specifically observed for the Paniceae tribe within the Panicoideae subfamily in grasses. Five SvLAC genes (SvLAC9, SvLAC13, SvLAC15, SvLAC50, and SvLAC52) fulfilled the criteria established to identify lignin-related candidates: (1) phylogenetic proximity to previously characterized lignin-related laccases from other species, (2) similar expression pattern to that observed for lignin biosynthetic genes in the S. viridis elongating internode, and (3) high expression in S. viridis tissues undergoing active lignification. In addition, in situ hybridization experiments not only confirmed that these selected SvLAC genes were expressed in lignifying cells, but also that their expression showed different tissue specificities, suggesting subfunctionalization events within the family. These five laccase genes are strong candidates to be involved in lignin polymerization in S. viridis and might be good targets for lignin bioengineering strategies.

Comparative transcriptome analysis of galls from four different host plants suggests the molecular mechanism of gall development

Galls are plant structures generated by gall–inducing organisms including insects, nematodes, fungi, bacteria and viruses. Those made by insects generally consist of inner callus–like cells surrounded by lignified hard cells, supplying both nutrients and protection to the gall insects living inside. This indicates that gall insects hijack developmental processes in host plants to generate tissues for their own use. Although galls are morphologically diverse, the molecular mechanism for their development remains poorly understood. To identify genes involved in gall development, we performed RNA–sequencing based transcriptome analysis for leaf galls. We examined the young and mature galls of Glochidion obovatum (Phyllanthaceae), induced by the micromoth Caloptilia cecidophora (Lepidoptera: Gracillariidae), the leaf gall from Eurya japonica (Pentaphylacaceae) induced by Borboryctis euryae (Lepidoptera: Gracillariidae), and the strawberry-shaped leaf gall from Artemisia montana (Asteraceae) induced by gall midge Rhopalomyia yomogicola (Oligotrophini: Cecidomyiidae). Gene ontology (GO) analyses suggested that genes related to developmental processes are up–regulated, whereas ones related to photosynthesis are down–regulated in these three galls. Comparison of transcripts in these three galls together with the gall on leaves of Rhus javanica (Anacardiaceae), induced by the aphid Schlechtendalia chinensis (Hemiptera: Aphidoidea), suggested 38 genes commonly up–regulated in galls from different plant species. GO analysis showed that peptide biosynthesis and metabolism are commonly involved in the four different galls. Our results suggest that gall development involves common processes across gall inducers and plant taxa, providing an initial step towards understanding how they manipulate host plant developmental systems.

Prediction of some peroxidase functions in <i>Arabidopsis thaliana</i> L. by bioinformatic search

Peroxidases of class III are common in various organisms. They are involved in lignin biosynthesis and plant protection against stressors. Peroxidases are presented in many isoforms, whose role is not always clear. The aim of this study is to analyze the amino acid sequences of reference peroxidases with known functions and peroxidases from Arabidopsis thaliana L. whose functions are unknown and to consider their putative roles in lignin biosynthesis. The structural and functional organization of peroxidases was analyzed by bioinformatical methods applied to open Internet sources. Seven reference peroxidases were chosen from four plant species: Zinnia sp., Armoracia rusticana P.G. Gaertn., Lycopersicon esculentum L. и Populus alba L. Twenty-four amino acid sequences of homologous peroxidases from A. thaliana were selected for the analyses with the BLAST service. Their molecular weights and isoelectric points were calculated. Multiple alignments of amino acid sequences and phylogenetic analysis were done. Sites of binding to monolignol substrates were identified in seven peroxidases from A. thaliana, and the enzymes were assigned to the groups of Sor G-peroxidases. Amino acid replacements in the primary structures of peroxidases were analyzed. Peroxidases from A. thaliana were clustered with reference peroxidases. They formed six clusters on the phylogenetic tree, three of which contained only A. thaliana peroxidases. Peroxidases within each cluster had similar molecular weights and isoelectric points, common localization of expression, and similar functions. Thus, the use of bioinformatics, databases, and published data bring us to assumptions as to the functions of several A. thaliana class III peroxidases. AtPrx39 peroxidase was shown to be affine to sinapyl alcohol; AtPrx54, to p-coumaryl and coniferyl alcohols. They are likely to participate in lignin biosynthesis.

Management of chromium (VI) toxicity by calcium and sulfur in tomato and brinjal: Implication of nitric oxide

To reduce pressure of toxic metals on crop plants, several strategies are being employed of which nutrient management is gaining much importance. Moreover, whether nitric oxide (NO), has any role in nutrients-mediated management/amelioration of metal toxicity is still not known. Therefore, the role of Ca and S in managing Cr(VI) toxicity was investigated in tomato and brinjal with an emphasis on possible involvement of NO. Cr(VI) reduced growth in both vegetables which was accompanied by increased accumulation of Cr(VI), lignin and reactive oxygen species (ROS), and altered cell cycle dynamics and photochemistry of photosynthesis. However, external addition of either Ca or S reversed these effects and hence improved growth noticed in both vegetables. Cr(VI) toxicity was further increased by NG-nitro-l-arginine methyl ester even with additional Ca and S while sodium nitroprusside either restored growth up to the control level or increased it in both vegetables, even in the presence of L-NAME, suggesting that NO might have a positive role in nutrients-mediated management/amelioration of Cr(VI) toxicity. In this study, role of Ca, S and NO with reference to Cr(VI) and NO accumulation, components of phenylpropanoid pathway, cell cycle dynamics, photosynthesis, ROS and antioxidant potential in managing Cr(VI) toxicity is discussed.

PbrmiR397a regulates lignification during stone cell development in pear fruit

Lignified stone cells substantially reduce fruit quality. Therefore, it is desirable to inhibit stone cell development using genetic technologies. However, the molecular mechanisms regulating lignification are poorly understood in fruit stone cells. In this study, we have shown that microRNA (miR) miR397a regulates fruit cell lignification by inhibiting laccase (LAC) genes that encode key lignin biosynthesis enzymes. Transient overexpression of PbrmiR397a, which is the miR397a of Chinese pear (Pyrus bretschneideri), and simultaneous silencing of three LAC genes reduced the lignin content and stone cell number in pear fruit. A single nucleotide polymorphism (SNP) identified in the promoter of the PbrmiR397a gene was found to associate with low levels of fruit lignin, after analysis of the genome sequences of sixty pear varieties. This SNP created a TCA element that responded to salicylic acid to induce gene expression as confirmed using a cell-based assay system. Furthermore, stable overexpression of PbrmiR397a in transgenic tobacco plants reduced the expression of target LAC genes and decreased the content of lignin but did not change the ratio of syringyl- and guaiacyl-lignin monomers. Consistent with reduction in lignin content, the transgenic plants showed fewer numbers of vessel elements and thinner secondary walls in the remaining elements compared to wild-type control plants. This study has advanced our understanding of the regulation of lignin biosynthesis and provided useful molecular genetic information for improving pear fruit quality.

The Casparian strip-one ring to bring cell biology to lignification?

Lignin research has long been motivated by the outstanding importance of wood for human societies. The annual, non-woody Arabidopsis thaliana, has nevertheless contributed greatly to our understanding of lignification, due to its unrivalled genetic resources. Arabidopsis is also great for cell and developmental biology, allowing precise imaging and tracking of cell types. Root endodermis differentiation involves the precise lignification of the Casparian Strip, as an apoplastic barrier; while barrier damage triggers a less localized, compensatory lignification. Transcriptional reprogramming and peptide-induced signalling emerge as promising tools for the study of endodermal lignification. We argue that endodermis lignification is an attractive model complementary to equally powerful, cellular xylem differentiation systems, as it might better represent the restricted - often localized - lignification seen in non-vascular cells.

Lignin polymerization: how do plants manage the chemistry so well?

The final step of lignin biosynthesis is the polymerization of monolignols in apoplastic cell wall domains. In this process, monolignols secreted by lignifying cells, or occasionally neighboring non-lignifying and/or other lignifying cells, are activated by cell-wall-localized oxidation systems, such as laccase/O₂ and/or peroxidase/H₂O₂, for combinatorial radical coupling to make the final lignin polymers. Plants can precisely control when, where, and which types of lignin polymers are assembled at tissue and cellular levels, but do not control the polymers' exact chemical structures per se. Recent studies have begun to identify specific laccase and peroxidase proteins responsible for lignin polymerization in specific cell types and during different developmental stages. The coordination of polymerization machinery localization and monolignol supply is likely critical for the spatio-temporal patterning of lignin polymerization. Further advancement in this research area will continue to increase our capacity to manipulate lignin content/structure in biomass to meet our own biotechnological purposes.

Class III peroxidases in cellulose deficient cultured maize cells during cell wall remodeling

Maize (Zea mays L.) suspension-cultured cells habituated to a cellulose biosynthesis inhibitor 2,6-dichlorobenzonitrile (DCB) have a modified cell wall, in which the reduction in the cellulose content is compensated by a network of highly cross-linked feruloylated arabinoxylans and the deposition of lignin-like polymers. For both arabinoxylan cross-linking and lignin polymerization, class III peroxidases (POXs) have been demonstrated to have a prominent role. For the first time, a comparative study of POX activity and isoforms in control and cellulose-impaired cells has been addressed, also taking into account their cellular distribution in different compartments. Proteins from the spent medium (SM), soluble cellular (SC), ionically (ICW) and covalently bound cell wall protein fractions were assayed for total and specific peroxidase activity by using coniferyl and sinapyl alcohol and ferulic acid as substrates. The isoPOX profile was obtained by isoelectric focusing. POX activity was higher in DCB-habituated than in non-habituated cells in all protein fractions at all cell culture stages. For all substrates assayed, SC and ICW fractions showed higher activity at the early log growth phase than at the late log phase. However, the highest POX activity in the spent medium was found at the late log phase. According to the isoPOX profiles, the highest diversity of isoPOXs was detected in the ICW and SM protein fractions. The latter fraction contained isoPOXs with higher activity in DCB-habituated cells. Some of the isoPOXs detected could be involved in cross-linking of arabinoxylans and in the lignin-like polymer formation in DCB-habituated cells.

Expression analysis of transporter genes for screening candidate monolignol transporters using Arabidopsis thaliana cell suspensions during tracheary element differentiation

The mechanism of monolignol transportation from the cytosol to the apoplast is still unclear despite being an essential step of lignification. Recently, ATP-binding cassette (ABC) transporters were suggested to be involved in monolignol transport. However, there are no reliable clues to the transporters of the major lignin monomers coniferyl and synapyl alcohol. In this study, the lignification progress of Arabidopsis cultured cells during tracheary element differentiation was monitored. The expression of selected transporter genes, as well as lignification and cell-wall formation related genes as references, in differentiating cultured cell samples harvested at 2-day intervals was analyzed by real-time PCR and the data were statistically processed. The cell wall formation transcription factor MYB46, programmed-cell death related gene XCP1 and lignin polymerization peroxidase AtPrx25 were classified into the same cluster. Furthermore, the cluster closest to the abovementioned cluster contained the lignin synthesis transcription factor MYB58 and the Arabidopsis ABC transporters ABCG11, ABCG22, ABCG36 and ABCG29. This result suggested that these four ABC transporters may be involved in lignification. In the expression analysis, unexpectedly, the lignification-related genes CAD5 and C4H were not included in the same cluster as MYB58 and AtPrx25. The expression data also suggested that the lignification of tracheary elements in the culture, where lignification ratio finally reached to around 40%, continued after cell death because lignification actively progressed after programmed cell death-related gene started to be expressed.

Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl

BACKGROUND

Lignin and lignans are both derived from the monolignol pathway. Despite the similarity of their building blocks, they fulfil different functions in planta. Lignin strengthens the tissues of the plant, while lignans are involved in plant defence and growth regulation. Their biosyntheses are tuned both spatially and temporally to suit the development of the plant (water conduction, reaction to stresses). We propose to study the general molecular events related to monolignol-derived product biosynthesis, especially lignin. It was previously shown that the growing hemp hypocotyl (between 6 and 20 days after sowing) is a valid system to study secondary growth and the molecular events accompanying lignification. The present work confirms the validity of this system, by using it to study the regulation of lignin and lignan biosynthesis. Microscopic observations, lignin analysis, proteomics, together with in situ laccase and peroxidase activity assays were carried out to understand the dynamics of lignin synthesis during the development of the hemp hypocotyl.

RESULTS

Based on phylogenetic analysis and targeted gene expression, we suggest a role for the hemp dirigent and dirigent-like proteins in lignan biosynthesis. The transdisciplinary approach adopted resulted in the gene- and protein-level quantification of the main enzymes involved in the biosynthesis of monolignols and their oxidative coupling (laccases and class III peroxidases), in lignin deposition (dirigent-like proteins) and in the determination of the stereoconformation of lignans (dirigent proteins).

CONCLUSIONS

Our work sheds light on how, in the growing hemp hypocotyl, the provision of the precursors needed to synthesize the aromatic biomolecules lignin and lignans is regulated at the transcriptional and proteomic level.

Increased cell wall thickness of endodermis and protoxylem in Aeluropus littoralis roots under salinity: The role of LAC4 and PER64 genes

Enhanced cell wall lignification is one of the major salinity tolerance strategies in the roots of halophytes. A deep insight into the exact root developmental system in halophytes may be of great importance for understanding plant salt tolerance mechanisms. In this work the developmental and anatomical changes in the roots of halophyte Aeluropus littoralis along with expression patterns of two genes encoding for cell wall laccase (LAC4) and peroxidase (PER64) were investigated. The plants were treated with 0, 300 and 600mM NaCl and root samples were collected 3, 6 and 9days after treatment (DAT). Upon salinity treatment, root diameter and parenchyma thickness were increased significantly in the tip and middle segments compared to upper zones, but the change trend was reversed with the time. It was interestingly revealed that protoxylem was the tissue of target for lignification at root tips, while the highest lignification rates were observed in metaxylem and endodermis in upper segments. Compared to endodermis, protoxylem is restrictively involved in early stages of salt stress in root tips as an efficient barrier against Na⁺ flow. Gene expression analysis revealed that LAC4 expression was higher in root tips resulting in enhanced protoxylem lignification while PER64 expression was higher in more differentiated zones leading to endodermis thickening. The overall results of this study reveal the crucial role of LAC4 as an important gene in specialized protoxylem lignification in undifferentiated root tips leading to enhanced tolerance in early stages of salt stress.

How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae?

The origin of land plants from algae is a long-standing question in evolutionary biology. It is becoming increasingly clear that many characters that were once assumed to be 'embryophyte specific' can in fact be found in their closest algal relatives, the streptophyte algae. One such case is the phenylpropanoid pathway. While biochemical data indicate that streptophyte algae harbor lignin-like components, the phenylpropanoid core pathway, which serves as the backbone of lignin biosynthesis, has been proposed to have arisen at the base of the land plants. Here we revisit this hypothesis using a wealth of new sequence data from streptophyte algae. Tracing the biochemical pathway towards lignin biogenesis, we show that most of the genes required for phenylpropanoid synthesis and the precursors for lignin production were already present in streptophyte algae. Nevertheless, phylogenetic analyses and protein structure predictions of one of the key enzyme classes in lignin production, cinnamyl alcohol dehydrogenase (CAD), suggest that CADs of streptophyte algae are more similar to sinapyl alcohol dehydrogenases (SADs). This suggests that the end-products of the pathway leading to lignin biosynthesis in streptophyte algae may facilitate the production of lignin-like compounds and defense molecules. We hypothesize that streptophyte algae already possessed the genetic toolkit from which the capacity to produce lignin later evolved in vascular plants.

BnLATE, a Cys2/His2-Type Zinc-Finger Protein, Enhances Silique Shattering Resistance by Negatively Regulating Lignin Accumulation in the Silique Walls of Brassica napus

Silique shattering resistance is one of the most important agricultural traits in oil crop breeding. Seed shedding from siliques prior to and during harvest causes devastating losses in oilseed yield. Lignin biosynthesis in the silique walls is thought to affect silique-shattering resistance in oil crops. Here, we identified and characterized B. napus LATE FLOWERING (BnLATE), which encodes a Cys2/His2-type zinc-finger protein. Heterologous expression of BnLATE under the double enhanced CaMV 35S promoter (D35S) in wild-type Arabidopsis plants resulted in a marked decrease in lignification in the replum, valve layer (carpel) and dehiscence zone. pBnLATE::GUS activity was strong in the yellowing silique walls of transgenic lines. Furthermore, the expression pattern of BnLATE and the lignin content gradient in the silique walls at 48 days after pollination (DAP) of 73290, a B. napus silique shattering-resistant line, are similar to those in transgenic Arabidopsis lines expressing BnLATE. Transcriptome sequencing of the silique walls revealed that genes encoding peroxidases, which polymerize monolignols and lignin in the phenylpropanoid pathway, were down-regulated at least two-fold change in the D35S::BnLATE transgenic lines. pBnLATE::BnLATE transgenic lines were further used to identify the function of BnLATE, and the results showed that lignification in the carpel and dehiscence zone of yellowing silique also remarkably decreased compared with the wild-type control, the silique shattering-resistance and expression pattern of peroxidase genes are very similar to results with D35S::BnLATE. These results suggest that BnLATE is a negative regulator of lignin biosynthesis in the yellowing silique walls, and promotes silique-shattering resistance in B. napus through restraining the polymerization of monolignols and lignin.

Extra-Cellular But Extra-Ordinarily Important for Cells: Apoplastic Reactive Oxygen Species Metabolism

Reactive oxygen species (ROS), by their very nature, are highly reactive, and it is no surprise that they can cause damage to organic molecules. In cells, ROS are produced as byproducts of many metabolic reactions, but plants are prepared for this ROS output. Even though extracellular ROS generation constitutes only a minor part of a cell's total ROS level, this fraction is of extraordinary importance. In an active apoplastic ROS burst, it is mainly the respiratory burst oxidases and peroxidases that are engaged, and defects of these enzymes can affect plant development and stress responses. It must be highlighted that there are also other less well-known enzymatic or non-enzymatic ROS sources. There is a need for ROS detoxification in the apoplast, and almost all cellular antioxidants are present in this space, but the activity of antioxidant enzymes and the concentration of low-mass antioxidants is very low. The low antioxidant efficiency in the apoplast allows ROS to accumulate easily, which is a condition for ROS signaling. Therefore, the apoplastic ROS/antioxidant homeostasis is actively engaged in the reception and reaction to many biotic and abiotic stresses.

The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation

Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.

Arabidopsis COGWHEEL1 links light perception and gibberellins with seed tolerance to deterioration

Light is a major regulator of plant growth and development by antagonizing gibberellins (GA), and we provide evidence for a role of light perception and GA in seed coat formation and seed tolerance to deterioration. We have identified two activation-tagging mutants of Arabidopsis thaliana, cog1-2D and cdf4-1D, with improved seed tolerance to deterioration linked to increased expression of COG1/DOF1.5 and CDF4/DOF2.3, respectively. These encode two homologous DOF transcription factors, with COG1 most highly expressed in seeds. Improved tolerance to seed deterioration was reproduced in transgenic plants overexpressing these genes, and loss of function from RNA interference resulted in opposite phenotypes. Overexpressions of COG1 and CDF4 have been described to attenuate various light responses mediated by phytochromes. Accordingly, we found that phyA and phyB mutants exhibit increased seed tolerance to deterioration. The phenotype of tolerance to deterioration conferred by gain of function of COG1 and by loss of function of phytochromes is of maternal origin, is also observed under natural aging conditions and correlates with a seed coat with increased suberin and reduced permeability. In developing siliques of the cog1-2D mutant the expression of the GA biosynthetic gene GA3OX3 and levels of GA1 are higher than in the wild type. These results explain the antagonism between phytochromes and COG1 in terms of the inhibition and the activation, respectively, of GA action.

Extraction and Characterization of Extracellular Proteins and Their Post-Translational Modifications from Arabidopsis thaliana Suspension Cell Cultures and Seedlings: A Critical Review

Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are constantly evolving to increase the number of proteins that can be detected and identified. In addition, the dynamic nature of the extracellular proteome presents the further challenge of identifying and characterizing the post-translational modifications (PTMs) of secreted proteins, particularly glycosylation and phosphorylation. Such PTMs are common and important regulatory modifications of proteins, playing a key role in many biological processes. This review explores the most recent methods in isolating and characterizing the plant extracellular proteome with a focus on the model plant Arabidopsis thaliana, highlighting the current challenges yet to be overcome. Moreover, the crucial role of protein PTMs in cell wall signalling, development, and plant responses to biotic and abiotic stress is discussed.

In situ detection of laccase activity and immunolocalisation of a compression-wood-specific laccase (CoLac1) in differentiating xylem of Chamaecyparis obtusa

The secondary cell wall of compression wood tracheids has a highly lignified region (S2L) in its outermost portion. To better understand the mechanism of S2L formation, we focussed on the activity of laccase (a monolignol oxidase) and performed in situ studies of this enzyme in differentiating compression wood. Staining of differentiating compression wood demonstrated that laccase activity began in all cell wall layers before the onset of lignification. We detected no activity of peroxidase (another monolignol oxidase) in any cell wall layer. Thus, laccase likely plays the major role in monolignol oxidisation during compression wood differentiation. Laccase activity was higher in the S2L region than in other secondary wall regions, suggesting that this enzyme was responsible for the high lignin concentration in this region of the cell wall. Immunolabelling demonstrated the expression of a compression-wood-specific laccase (CoLac1) immediately following the onset of secondary wall thickening, this enzyme was localised to the S2L region, whereas much less abundant in the S1 layer or inner S2 layer. Thus, the CoLac1 protein is most likely localised to the outer part of S2 and responsible for the high lignin concentration in the S2L region.

Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis

Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.

Suppression of Arabidopsis peroxidase 72 alters cell wall and phenylpropanoid metabolism

Class III peroxidases are glycoproteins with a major role in cell wall maturation such as lignin formation. Peroxidases are usually present in a high number of isoenzymes, which complicates to assign specific functions to individual peroxidase isoenzymes. Arabidopsis genome encodes for 73 peroxidases, among which AtPrx72 has been shown to participate in lignification. Here, we report by using knock out peroxidase mutants how the disruption of AtPrx72 causes thinner secondary walls in interfascicular fibres but not in the xylem of the stem. This effect is also age-dependent, and AtPrx72 function seems to be particularly important when lignification prevails over elongation processes. Finally, the suppression AtPrx72 leads to the down-regulation of lignin biosynthesis pathway, as well as genes and transcription factors involved in secondary wall thickening.

The cell biology of lignification in higher plants

BACKGROUND

Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying.

SCOPE

Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level.

CONCLUSIONS

The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.

Norway spruce (Picea abies) laccases: characterization of a laccase in a lignin-forming tissue culture

Secondarily thickened cell walls of water-conducting vessels and tracheids and support-giving sclerenchyma cells contain lignin that makes the cell walls water impermeable and strong. To what extent laccases and peroxidases contribute to lignin biosynthesis in muro is under active evaluation. We performed an in silico study of Norway spruce (Picea abies (L.) Karst.) laccases utilizing available genomic data. As many as 292 laccase encoding sequences (genes, gene fragments, and pseudogenes) were detected in the spruce genome. Out of the 112 genes annotated as laccases, 79 are expressed at some level. We isolated five full-length laccase cDNAs from developing xylem and an extracellular lignin-forming cell culture of spruce. In addition, we purified and biochemically characterized one culture medium laccase from the lignin-forming cell culture. This laccase has an acidic pH optimum (pH 3.8-4.2) for coniferyl alcohol oxidation. It has a high affinity to coniferyl alcohol with an apparent Km value of 3.5 μM; however, the laccase has a lower catalytic efficiency (V(max)/K(m)) for coniferyl alcohol oxidation compared with some purified culture medium peroxidases. The properties are discussed in the context of the information already known about laccases/coniferyl alcohol oxidases of coniferous plants.

Roles of cell wall peroxidases in plant development

Class III peroxidases (CIII Prxs) are plant specific proteins. Based on in silico prediction and experimental evidence, they are mainly considered as cell wall localized proteins. Thanks to their dual hydroxylic and peroxidative cycles, they can produce ROS as well as oxidize cell wall aromatic compounds within proteins and phenolics that are either free or linked to polysaccharides. Thus, they are tightly associated to cell wall loosening and stiffening. They are members of large multigenic families, mostly due to an elevated rate of gene duplication in higher plants, resulting in a high risk of functional redundancy between them. However, proteomic and (micro)transcriptomic analyses have shown that CIII Prx expression profiles are highly specific. Based on these omic analyses, several reverse genetic studies have demonstrated the importance of the spatio-temporal regulation of their expression and ability to interact with cell wall microdomains in order to achieve specific activity in vivo. Each CIII Prx isoform could have specific functions in muro and this could explain the conservation of a high number of genes in plant genomes.

Simultaneously disrupting AtPrx2, AtPrx25 and AtPrx71 alters lignin content and structure in Arabidopsis stem

Plant class III heme peroxidases catalyze lignin polymerization. Previous reports have shown that at least three Arabidopsis thaliana peroxidases, AtPrx2, AtPrx25 and AtPrx71, are involved in stem lignification using T-DNA insertion mutants, atprx2, atprx25, and atprx71. Here, we generated three double mutants, atprx2/atprx25, atprx2/atprx71, and atprx25/atprx71, and investigated the impact of the simultaneous deficiency of these peroxidases on lignins and plant growth. Stem tissue analysis using the acetyl bromide method and derivatization followed by reductive cleavage revealed improved lignin characteristics, such as lowered lignin content and increased arylglycerol-β-aryl (β-O-4) linkage type, especially β-O-4 linked syringyl units, in lignin, supporting the roles of these genes in lignin polymerization. In addition, none of the double mutants exhibited severe growth defects, such as shorter plant stature, dwarfing, or sterility, and their stems had improved cell wall degradability. This study will contribute to progress in lignin bioengineering to improve lignocellulosic biomass.

Ectopic lignification in the flax lignified bast fiber1 mutant stem is associated with tissue-specific modifications in gene expression and cell wall composition

Histochemical screening of a flax ethyl methanesulfonate population led to the identification of 93 independent M2 mutant families showing ectopic lignification in the secondary cell wall of stem bast fibers. We named this core collection the Linum usitatissimum (flax) lbf mutants for lignified bast fibers and believe that this population represents a novel biological resource for investigating how bast fiber plants regulate lignin biosynthesis. As a proof of concept, we characterized the lbf1 mutant and showed that the lignin content increased by 350% in outer stem tissues containing bast fibers but was unchanged in inner stem tissues containing xylem. Chemical and NMR analyses indicated that bast fiber ectopic lignin was highly condensed and rich in G-units. Liquid chromatography-mass spectrometry profiling showed large modifications in the oligolignol pool of lbf1 inner- and outer-stem tissues that could be related to ectopic lignification. Immunological and chemical analyses revealed that lbf1 mutants also showed changes to other cell wall polymers. Whole-genome transcriptomics suggested that ectopic lignification of flax bast fibers could be caused by increased transcript accumulation of (1) the cinnamoyl-CoA reductase, cinnamyl alcohol dehydrogenase, and caffeic acid O-methyltransferase monolignol biosynthesis genes, (2) several lignin-associated peroxidase genes, and (3) genes coding for respiratory burst oxidase homolog NADPH-oxidases necessary to increase H2O2 supply.