Cell wall integrity regulation across plant species

Impact of m6A modification and transcript quantity on mRNA composition in plant stress granules under hypoxia

Stress granules (SGs) are cytoplasmic structures that appear in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood, and despite the recognized role of N6-methyladenosine (m6A) in plant transcriptome regulation, its impact on SG composition and assembly remains unknown. In Lupinus angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in their ultrastructure and composition. Following a transcriptome analysis, specific mRNAs were chosen to investigate their localization within SGs and to assess m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, was present both in the SGs and the cytoplasm, probably due to an extremely high expression level. The m6A modification was observed only during the assembly of SGs. In mutants of Arabidopsis with reduced levels of m6A, ECT2 (a reader of m6A) was not observed in SGs, and poly(A) RNA levels and the number of SGs were reduced. Our findings thus demonstrate a limited impact of m6A modification on SG assembly; however, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs.

Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis

Understanding how plants adapt their physiology to overcome severe and often multifactorial stress conditions in nature is vital in light of the climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms. To provide a comprehensive picture of stress-mitigation mechanisms, an exhaustive analysis of publicly available stress-related transcriptomic data has been conducted. We combine a meta-analysis with an unsupervised machine-learning algorithm to identify a core of stress-related genes active at 1-6 h and 12-24 h of exposure in Arabidopsis thaliana shoots and roots. To ensure robustness and biological significance of the output, often lacking in meta-analyses, a triple validation is incorporated. We present a 'stress gene core': a set of key genes involved in plant tolerance to ten adverse environmental conditions and ethylene-precursor supplementation rather than individual conditions. Notably, ethylene plays a key regulatory role in this core, influencing gene expression and acting as a critical factor in stress tolerance. Additionally, the analysis provides insights into previously uncharacterized genes, key genes within large families, and gene expression dynamics, which are used to create biologically validated databases that can guide further abiotic stress research. These findings establish a strong framework for advancing multi-stress-resilient crops, paving the way for sustainable agriculture in the face of climate challenges.

Transcriptome profiling reveals abnormal cell wall components in the cleistogamy mutant 1 (clm1) lodicule of foxtail millet

MAIN CONCLUSION

The molecular mechanism of cleistogamy in foxtail millet was analyzed. We found that changes of cell wall components caused the abnormal development of the lodicule. Outcrossing between cultivated crops and their associated wild species may result in the loss of favorable agricultural traits in the progeny or the drift of genetically modified (GM) organisms in future generations. In this study, we found a cleistogamy mutant with an abnormal development of the lodicules. The lodicules were sampled when the florets just to bloom for RNA-seq analysis. Our results showed that, compared with the wild type, the mutant had more enriched pathways related to cell wall synthesis or decomposition. Staining of the lodicule cell wall showed that the mutant had relatively lower amounts of callose and cellulose than the wild type. The content of pectin methylation in the lodicule cell wall of the mutant was lower than that of the wild type. In summary, we analyzed the causes of cleistogamy phenotype in foxtail millet. Transcriptome data analysis revealed that this was probably caused by dysplasia of the lodicule cell wall. Cytochemical staining and immunofluorescence tests showed that the changes of the components in the cell wall caused the abnormal development of the lodicule. Overall, this study sheds light on the potential molecular mechanism of cleistogamy of foxtail millet and provides a theoretical basis for subsequent research.

Systems Biology of Streptophyte Cell Evolution

More than 500 million years ago, a streptophyte algal population established a foothold on land and started terraforming Earth through an unprecedented radiation. This event is called plant terrestrialization and yielded the Embryophyta. Recent advancements in the field of plant evolutionary developmental biology (evo-devo) have propelled our knowledge of the closest algal relatives of land plants, the zygnematophytes, highlighting that several aspects of plant cell biology are shared between embryophytes and their sister lineage. High-throughput exploration determined that routes of signaling cascades, biosynthetic pathways, and molecular physiology predate plant terrestrialization. But how do they assemble into biological programs, and what do these programs tell us about the principal functions of the streptophyte cell? Here, we make the case that streptophyte algae are unique organisms for understanding the systems biology of the streptophyte cell, informing on not only the origin of embryophytes but also their fundamental biology.

Peptides and Reactive Oxygen Species Regulate Root Development

Like phytohormones, peptide hormones participate in many cellular processes, participate in intercellular communications, and are involved in signal transmission. The system of intercellular communications based on peptide-receptor interactions plays a critical role in the development and functioning of plants. One of the most important molecules are reactive oxygen species (ROS). ROS participate in signaling processes and intercellular communications, including the development of the root system. ROS are recognized as active regulators of cell division and differentiation, which depend on the oxidation-reduction balance. The stem cell niche and the size of the root meristem are maintained by the intercellular interactions and signaling networks of peptide hormone and ROS. Therefore, peptides and ROS can interact with each other both directly and indirectly and function as regulators of cellular processes. Peptides and ROS regulate cell division and stem cell differentiation through a negative feedback mechanism. In this review, we focused on the molecular mechanisms regulating the development of the main root, lateral roots, and nodules, in which peptides and ROS participate.

Aberrant growth and expansion in Penium margaritaceum triggered by disruption of microtubules and the cell wall

Penium margaritaceum, a unicellular zygnematophyte (Streptophyta), was employed to elucidate changes in cell expansion when cells were challenged with the fungal pectinolytic enzyme, pectate lyase, and/or the microtubule-disrupting agent, amiprophos-methyl (APM). Microtubule disruption by APM resulted in significant swelling at expansion zones. These swollen zones provided an easy marker for the location of expansion zones, particularly in cells with altered cell wall pectin. Short-term treatment with pectate lyase showed pectin degradation primarily at the isthmus expansion zone and two satellite bands, corresponding to the location of future expansion in daughter cells. When the homogalacturonan lattice of the cell wall was removed by treatment with pectate lyase during long treatments, cell division was maintained, but daughter cell products were considerably smaller. Treatment of cells with a mixture of both pectate lyase and APM resulted in a distinct phenotype, consisting of 'dumbbell'-shaped cells, as APM-induced swelling occurs at the novel expansion centers exposed by pectate lyase treatment. These cells also presented other curious alterations, including an extensive, chloroplast-free cytoplasmic zone at the center of the cell, a septum containing β-glycan, arabinogalactan and homogalacturonan epitopes, unique stacks of endoplasmic reticulum, displaced Golgi bodies, and an extensive network of vacuoles. These results provide insight into the importance of cell wall integrity in defining the location of cell growth and division in P. margaritaceum. Understanding these processes in a unicellular zygnematophyte may provide insights into steps involved in the evolution of land plants.

Identification and characterization of the auxin-response factor family in moso bamboo reveals that PeARF41 negatively regulates second cell wall formation

Auxin response factors (ARFs) are key transcriptional factors mediating the transcriptional of auxin-related genes that play crucial roles in a range of plant metabolic activities. The characteristics of 47 PeARFs, identified in moso bamboo and divided into three classes, were evaluated. Structural feature analysis showed that intron numbers ranged from 3 to 14, while Motif 1, 2, 7 and 10 were highly conserved, altogether forming DNA-binding and ARF domains. Analysis of RNA-seq from different tissues revealed that PeARFs showed tissue-specificity. Additionally, abundant hormone-response and stress-related elements were enriched in promoters of PeARFs, supporting the hypothesis that the expression of PeARFs was significantly activated or inhibited by ABA and cold treatments. Further, PeARF41 overexpression inhibited SCW formation by reducing hemicellulose, cellulose and lignin contents. Moreover, a co-expression network, containing 28 genes with PeARF41 at its core was predicted, and the results of yeast one hybridization (Y1H), electrophoretic mobility shift assay (EMSA) and dual-luciferase (Dul-LUC) assays showed that PeARF41 bound the PeSME1 promoter to inhibit its expression. We conclude that a 'PeARF41-PeSME1' regulatory cascade mediates SCW formation. Our findings provided a solid theoretical foundation for further research on the role of PeARFs.

ATG8ylation of vacuolar membrane protects plants against cell wall damage

Vacuoles are essential for cellular metabolism and growth and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity have remained elusive in plants. Here we describe a conserved vacuolar quality control pathway that is activated upon cell wall damage in a turgor-pressure-dependent manner. Cell wall perturbations induce a distinct modification-ATG8ylation-on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage.

Cell walls, a comparative view of the composition of cell surfaces of plants, algae and microorganisms

While evolutionary studies indicate that the most ancient groups of organisms on Earth likely descended from a common wall-less ancestor, contemporary organisms lacking a carbohydrate-rich cell surface are exceedingly rare. By developing a cell wall to cover the plasma membrane, cells were able to withstand higher osmotic pressures, colonise new habitats and develop complex multicellular structures. This way, the cells of plants, algae and microorganisms are covered by a cell wall, which can generally be defined as a highly complex structure whose main framework is usually composed of carbohydrates. Rather than static structures, they are highly dynamic and serve a multitude of functions that modulate vital cellular processes, such as growth and interactions with neighbouring cells or the surrounding environment. Thus, despite its vital importance for many groups of life, it is striking that there are few comprehensive documents comparing the cell wall composition of these groups. Thus, the aim of this review was to compare the cell walls of plants with those of algae and microorganisms, paying particular attention to their polysaccharide components. It should be highlighted that, despite the important differences in composition, we have also found numerous common aspects and functionalities.

Plant cell walls: source of carbohydrate-based signals in plant-pathogen interactions

Plant cell walls are essential elements for disease resistance that pathogens need to overcome to colonise the host. Certain pathogens secrete a large battery of enzymes to hydrolyse plant cell wall polysaccharides, which leads to the release of carbohydrate-based molecules (glycans) that are perceived by plant pattern recognition receptors and activate pattern-triggered immunity and disease resistance. These released glycans are used by colonizing microorganisms as carbon source, chemoattractants to locate entry points at plant surface, and as signals triggering gene expression reprogramming. The release of wall glycans and their perception by plants and microorganisms determines plant-microbial interaction outcome. Here, we summarise and discuss the most recent advances in these less explored aspects of plant-microbe interaction.

Metal oxide nanoparticles as a promising method to reduce biotic stress in plant cell wall: A review

The application of metal-based nanoparticles in inhibiting plant pathogenic bacteria and fungi has gained significant attention in recent years. several nanoparticles, including silver (Ag), titanium dioxide (TiO2), magnesium oxide (MgO), copper (Cu), and zinc oxide (ZnO), can generate reactive oxygen species (ROS) when exposed to light. The oxidative damage inflicted by ROS can disrupt the cellular structures and metabolic processes of pathogens, leading to their inactivation and inhibition. However, it is crucial to consider the potential environmental and health impacts of nanoparticle use. The safe and responsible use of nanoparticles and their potential risks should be thoroughly evaluated to ensure sustainable and effective plant disease management practices.

Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity

The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.

Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato

BACKGROUND

During male gametogenesis of flowering plants, sperm cell lineage (microspores, generative cells, and sperm cells) differentiated from somatic cells and acquired different cell fates. Trimethylation of histone H3 on lysine 4 (H3K4me3) epigenetically contributes to this process, however, it remained unclear how H3K4me3 influences the gene expression in each cell type. Here, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) to obtain a genome-wide landscape of H3K4me3 during sperm cell lineage development in tomato (Solanum lycopersicum).

RESULTS

We show that H3K4me3 peaks were mainly enriched in the promoter regions, and intergenic H3K4me3 peaks expanded as sperm cell lineage differentiated from somatic cells. H3K4me3 was generally positively associated with transcript abundance and served as a better indicator of gene expression in somatic and vegetative cells, compared to sperm cell lineage. H3K4me3 was mutually exclusive with DNA methylation at 3' proximal of the transcription start sites. The microspore maintained the H3K4me3 features of somatic cells, while generative cells and sperm cells shared an almost identical H3K4me3 pattern which differed from that of the vegetative cell. After microspore division, significant loss of H3K4me3 in genes related to brassinosteroid and cytokinin signaling was observed in generative cells and vegetative cells, respectively.

CONCLUSIONS

Our results suggest the asymmetric division of the microspore significantly reshapes the genome-wide distribution of H3K4me3. Selective loss of H3K4me3 in genes related to hormone signaling may contribute to functional differentiation of sperm cell lineage. This work provides new resource data for the epigenetic studies of gametogenesis in plants.

Modifying lignin composition and xylan O-acetylation induces changes in cell wall composition, extractability, and digestibility

BACKGROUND

Lignin and xylan are important determinants of cell wall structure and lignocellulosic biomass digestibility. Genetic manipulations that individually modify either lignin or xylan structure improve polysaccharide digestibility. However, the effects of their simultaneous modifications have not been explored in a similar context. Here, both individual and combinatorial modification in xylan and lignin was studied by analysing the effect on plant cell wall properties, biotic stress responses and integrity sensing.

RESULTS

Arabidopsis plant co-harbouring mutation in FERULATE 5-HYDROXYLASE (F5H) and overexpressing Aspergillus niger acetyl xylan esterase (35S:AnAXE1) were generated and displayed normal growth attributes with intact xylem architecture. This fah1-2/35S:AnAXE1 cross was named as hyper G lignin and hypoacetylated (HrGHypAc) line. The HrGHypAc plants showed increased crystalline cellulose content with enhanced digestibility after chemical and enzymatic pre-treatment. Moreover, both parents and HrGHypAc without and after pre-treating with glucuronyl esterase and alpha glucuronidase exhibited an increase in xylose release after xylanase digestion as compared to wild type. The de-pectinated fraction in HrGHypAc displayed elevated levels of xylan and cellulose. Furthermore, the transcriptomic analysis revealed differential expression in cell wall biosynthetic, transcription factors and wall-associated kinases genes implying the role of lignin and xylan modification on cellular regulatory processes.

CONCLUSIONS

Simultaneous modification in xylan and lignin enhances cellulose content with improved saccharification efficiency. These modifications loosen cell wall complexity and hence resulted in enhanced xylose and xylobiose release with or without pretreatment after xylanase digestion in both parent and HrGHypAc. This study also revealed that the disruption of xylan and lignin structure is possible without compromising either growth and development or defense responses against Pseudomonas syringae infection.

Plant cell wall-mediated disease resistance: Current understanding and future perspectives

Beyond their function as structural barriers, plant cell walls are essential elements for the adaptation of plants to environmental conditions. Cell walls are dynamic structures whose composition and integrity can be altered in response to environmental challenges and developmental cues. These wall changes are perceived by plant sensors/receptors to trigger adaptative responses during development and upon stress perception. Plant cell wall damage caused by pathogen infection, wounding, or other stresses leads to the release of wall molecules, such as carbohydrates (glycans), that function as damage-associated molecular patterns (DAMPs). DAMPs are perceived by the extracellular ectodomains (ECDs) of pattern recognition receptors (PRRs) to activate pattern-triggered immunity (PTI) and disease resistance. Similarly, glycans released from the walls and extracellular layers of microorganisms interacting with plants are recognized as microbe-associated molecular patterns (MAMPs) by specific ECD-PRRs triggering PTI responses. The number of oligosaccharides DAMPs/MAMPs identified that are perceived by plants has increased in recent years. However, the structural mechanisms underlying glycan recognition by plant PRRs remain limited. Currently, this knowledge is mainly focused on receptors of the LysM-PRR family, which are involved in the perception of various molecules, such as chitooligosaccharides from fungi and lipo-chitooligosaccharides (i.e., Nod/MYC factors from bacteria and mycorrhiza, respectively) that trigger differential physiological responses. Nevertheless, additional families of plant PRRs have recently been implicated in oligosaccharide/polysaccharide recognition. These include receptor kinases (RKs) with leucine-rich repeat and Malectin domains in their ECDs (LRR-MAL RKs), Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE group (CrRLK1L) with Malectin-like domains in their ECDs, as well as wall-associated kinases, lectin-RKs, and LRR-extensins. The characterization of structural basis of glycans recognition by these new plant receptors will shed light on their similarities with those of mammalians involved in glycan perception. The gained knowledge holds the potential to facilitate the development of sustainable, glycan-based crop protection solutions.

Insights into the cell-wall dynamics in grapevine berries during ripening and in response to biotic and abiotic stresses

The cell wall (CW) is the dynamic structure of a plant cell, acting as a barrier against biotic and abiotic stresses. In grape berries, the modifications of pulp and skin CW during softening ensure flexibility during cell expansion and determine the final berry texture. In addition, the CW of grape berry skin is of fundamental importance for winemaking, controlling secondary metabolite extractability. Grapevine varieties with contrasting CW characteristics generally respond differently to biotic and abiotic stresses. In the context of climate change, it is important to investigate the CW dynamics occurring upon different stresses, to define new adaptation strategies. This review summarizes the molecular mechanisms underlying CW modifications during grapevine berry fruit ripening, plant-pathogen interaction, or in response to environmental stresses, also considering the most recently published transcriptomic data. Furthermore, perspectives of new biotechnological approaches aiming at modifying the CW properties based on other crops' examples are also presented.

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Genome-wide association study for yield-related traits in faba bean (Vicia faba L.)

Yield is the most complex trait to improve crop production, and identifying the genetic determinants for high yield is a major issue in breeding new varieties. In faba bean (Vicia faba L.), quantitative trait loci (QTLs) have previously been detected in studies of biparental mapping populations, but the genes controlling the main trait components remain largely unknown. In this study, we investigated for the first time the genetic control of six faba bean yield-related traits: shattering (SH), pods per plant (PP), seeds per pod (SP), seeds per plant (SPL), 100-seed weight (HSW), and plot yield (PY), using a genome-wide association study (GWAS) on a worldwide collection of 352 homozygous faba bean accessions with the aim of identifying markers associated with them. Phenotyping was carried out in field trials at three locations (Spain, United Kingdom, and Serbia) over 2 years. The faba bean panel was genotyped with the Affymetrix faba bean SNP-chip yielding 22,867 SNP markers. The GWAS analysis identified 112 marker-trait associations (MTAs) in 97 candidate genes, distributed over the six faba bean chromosomes. Eight MTAs were detected in at least two environments, and five were associated with multiple traits. The next step will be to validate these candidates in different genetic backgrounds to provide resources for marker-assisted breeding of faba bean yield.

The impact of insect egg deposition on Pinus sylvestris transcriptomic and phytohormonal responses to larval herbivory

Plants can improve their resistance to feeding damage by insects if they have perceived insect egg deposition prior to larval feeding. Molecular analyses of these egg-mediated defence mechanisms have until now focused on angiosperm species. It is unknown how the transcriptome of a gymnosperm species responds to insect eggs and subsequent larval feeding. Scots pine (Pinus sylvestris L.) is known to improve its defences against larvae of the herbivorous sawfly Diprion pini L. if it has previously received sawfly eggs. Here, we analysed the transcriptomic and phytohormonal responses of Scots pine needles to D. pini eggs (E-pine), larval feeding (F-pine) and to both eggs and larval feeding (EF-pine). Pine showed strong transcriptomic responses to sawfly eggs and-as expected-to larval feeding. Many egg-responsive genes were also differentially expressed in response to feeding damage, and these genes play an important role in biological processes related to cell wall modification, cell death and jasmonic acid signalling. EF-pine showed fewer transcriptomic changes than F-pine, whereas EF-treated angiosperm species studied so far showed more transcriptional changes to the initial phase of larval feeding than only feeding-damaged F-angiosperms. However, as with responses of EF-angiosperms, EF-pine showed higher salicylic acid concentrations than F-pine. Based on the considerable overlap of the transcriptomes of E- and F-pine, we suggest that the weaker transcriptomic response of EF-pine than F-pine to larval feeding damage is compensated by the strong, egg-induced response, which might result in maintained pine defences against larval feeding.

Uncovering the dominant role of root lignin accumulation in silicon-induced resistance to drought in tomato

The role of lignin accumulation in silicon-induced resistance has not been fully elucidated. Based on the finding that the root cell wall is protected by silicon, this study explored the role of lignin accumulation in silicon-induced drought resistance in tomato. The decreased silicon concentration of the root confirmed the dominant role of lignin accumulation in silicon-induced drought resistance. The lignin monomer content in the root was enhanced by silicon, and was accompanied by the enhancement of drought resistance. Histochemical and transcriptional analyses of lignin showed that lignin accumulation was promoted by silicon under drought stress. In addition, in the root zone, silicon-induced lignin accumulation increased as the distance from the root tip increased under drought stress. Surprisingly, the Dwarf gene was upregulated by silicon in the roots. Micro Tom Dwarf gene mutation and Micro Tom-d + Dwarf gene functional complementation were further used to confirm that Dwarf regulates the spatial accuracy of SHR expression in the root. Therefore, root lignin accumulation plays a dominant role in silicon-induced drought resistance in tomato and the regulation of spatial accuracy of root lignification by silicon under drought stress is through the BR pathway, thereby avoiding the inhibition of root growth caused by root lignification.

Transcriptome Analysis Reveals Drought-Responsive Pathways and Key Genes of Two Oat (Avena sativa) Varieties

To cope with the yield loss caused by drought stress, new oat varieties with greater drought tolerance need to be selected. In this study, two oat varieties with different drought tolerances were selected for analysis of their phenotypes and physiological indices under moderate and severe soil drought stress. The results revealed significant differences in the degree of wilting, leaf relative water content (RWC), and SOD and CAT activity between the two oat genotypes under severe soil drought stress; moreover, the drought-tolerant variety exhibited a significant increase in the number of stomata and wax crystals on the surface of both the leaf and guard cells; additionally, the morphology of the guard cells was normal, and there was no significant disruption of the grana lamella membrane or the nuclear envelope. Furthermore, transcriptome analysis revealed that the expression of genes related to the biosynthesis of waxes and cell-wall components, as well as those of the WRKY family, significantly increased in the drought-tolerant variety. These findings suggest that several genes involved in the antioxidant pathway could improve drought tolerance in plants by regulating the increase/decrease in wax and cell-wall constituents and maintaining normal cellular water potential, as well as improving the ability of the antioxidant system to scavenge peroxides in oats.

Microscale Thermophoresis (MST) to Study Rapid Alkalinization Factor (RALF)-Receptor Interactions

Microscale thermophoresis (MST) is a simple but powerful tool to study the in vitro interaction among biomolecules, and to quantify binding affinities. MST curves describe the change in the fluorescence level of a fluorescent target as a result of an IR-laser-induced temperature change. The degree and nature of the change in fluorescence signal depends on the size, charge, and solvation shell of the molecules, properties that change in function of the binding of a ligand to the fluorescent target.We used MST to describe the interaction between components of a regulatory module involved in plant cell wall integrity control. This module comprises the secreted peptide Rapid Alkalinization Factor 23 (RALF23) and its receptor complex consisting of the GPI-anchored receptor Lorelei-Like Glycoprotein 1 (LLG1) and a receptor kinase of the CrRLK1L family, FERONIA. Here we show how MST can also be used to study three-partner interactions.

A novel pectin methylesterase inhibitor, PMEI3, in common bean suggests a key role of pectin methylesterification in Pseudomonas resistance

The mechanisms underlying susceptibility to and defense against Pseudomonas syringae (Pph) of the common bean (Phaseolus vulgaris) have not yet been clarified. To investigate these, 15-day-old plants of the variety Riñón were infected with Pph and the transcriptomic changes at 2 h and 9 h post-infection were analysed. RNA-seq analysis showed an up-regulation of genes involved in defense/signaling at 2 h, most of them being down-regulated at 9 h, suggesting that Pph inhibits the transcriptomic reprogramming of the plant. This trend was also observed in the modulation of 101 cell wall-related genes. Cell wall composition changes at early stages of Pph infection were associated with homogalacturonan methylation and the formation of egg boxes. Among the cell wall genes modulated, a pectin methylesterase inhibitor 3 (PvPMEI3) gene, closely related to AtPMEI3, was detected. PvPMEI3 protein was located in the apoplast and its pectin methylesterase inhibitory activity was demonstrated. PvPMEI3 seems to be a good candidate to play a key role in Pph infection, which was supported by analysis of an Arabidopsis pmei3 mutant, which showed susceptibility to Pph, in contrast to resistant Arabidopsis Col-0 plants. These results indicate a key role of the degree of pectin methylesterification in host resistance to Pph during the first steps of the attack.

Root Colonization by Trichoderma atroviride Triggers Induced Systemic Resistance Primarily Independent of the Chitin-mediated Signaling Pathway in Arabidopsis

Beneficial root endophytic fungi induce systemic responses, growth promotion, and induced systemic resistance (ISR) in colonized host plants. The soil application of chitin, a main component of fungal cell walls, also systemically induces disease resistance. Therefore, chitin recognition and its downstream signaling pathway mediate ISR triggered by beneficial fungi colonizing the root. The present study compared systemic disease resistance and transcriptional responses induced by Trichoderma, a representative beneficial root endophytic fungus, and chitin in Arabidopsis. Significant plant growth promotion was observed under root colonization by the three beneficial fungi tested: Trichoderma atroviride, Serendipita indica, and S. vermifera. Only T. atroviride and S. indica triggered ISR against the necrotrophic fungal pathogen Alternaria brassicicola. Induced systemic resistance triggered by T. atroviride was compromised in the chitin-receptor mutant, whereas systemic resistance caused by the soil application of chitin was not. A transcriptome ana-lysis demonstrated that chitin-regulated genes were mostly shared with those regulated by T. atroviride; however, many of the latter were specific. The commonly enriched gene ontologies for these genes indicated that the T. atroviride inoculation and chitin application systemically controlled similar transcriptional responses, mainly associated with cell wall functions. Therefore, Trichoderma may trigger ISR primarily independent of the chitin-mediated signaling pathway; however, chitin and Trichoderma may systemically induce similar cellular functions aboveground.

The damage-associated molecular pattern cellotriose alters the phosphorylation pattern of proteins involved in cellulose synthesis and trans-Golgi trafficking in Arabidopsis thaliana

We have recently demonstrated that the cellulose breakdown product cellotriose is a damage-associated molecular pattern (DAMP) which induces responses related to the integrity of the cell wall. Activation of downstream responses requires the Arabidopsis malectin domain-containing CELLOOLIGOMER RECEPTOR KINASE1 (CORK1)¹. The cellotriose/CORK1 pathway induces immune responses, including NADPH oxidase-mediated reactive oxygen species production, mitogen-activated protein kinase 3/6 phosphorylation-dependent defense gene activation, and the biosynthesis of defense hormones. However, apoplastic accumulation of cell wall breakdown products should also activate cell wall repair mechanisms. We demonstrate that the phosphorylation pattern of numerous proteins involved in the accumulation of an active cellulose synthase complex in the plasma membrane and those for protein trafficking to and within the trans-Golgi network (TGN) are altered within minutes after cellotriose application to Arabidopsis roots. The phosphorylation pattern of enzymes involved in hemicellulose or pectin biosynthesis and the transcript levels for polysaccharide-synthesizing enzymes responded barely to cellotriose treatments. Our data show that the phosphorylation pattern of proteins involved in cellulose biosynthesis and trans-Golgi trafficking is an early target of the cellotriose/CORK1 pathway.

Origin, evolution, and diversification of the wall-associated kinase gene family in plants

KEY MESSAGE

The study of the origin, evolution, and diversification of the wall-associated kinase gene family in plants facilitates their functional investigations in the future. Wall-associated kinases (WAKs) make up one subfamily of receptor-like kinases (RLKs), and function directly in plant cell elongation and responses to biotic and abiotic stresses. The biological functions of WAKs have been extensively characterized in angiosperms; however, the origin and evolutionary history of the WAK family in green plants remain unclear. Here, we performed a comprehensive analysis of the WAK family to reveal its origin, evolution, and diversification in green plants. In total, 1061 WAK genes were identified in 37 species from unicellular algae to multicellular plants, and the results showed that WAK genes probably originated before bryophyte differentiation and were widely distributed in land plants, especially angiosperms. The phylogeny indicated that the land plant WAKs gave rise to five clades and underwent lineage-specific expansion after species differentiation. Cis-acting elements and expression patterns analyses of WAK genes in Arabidopsis and rice demonstrated the functional diversity of WAK genes in these two species. Many gene gains and losses have occurred in angiosperms, leading to an increase in the number of gene copies. The evolutionary trajectory of the WAK family during polyploidization was uncovered using Gossypium species. Our results provide insights into the evolution of WAK genes in green plants, facilitating their functional investigations in the future.

Jackfruit: Composition, structure, and progressive collapsibility in the largest fruit on the Earth for impact resistance

The jackfruit is the largest fruit on the Earth, reaching upwards of 35 kg and falling from heights of 25 m. To survive such high energy impacts, it has evolved a unique layered configuration with a thorny exterior and porous tubular underlayer. During compression, these layers exhibit a progressive collapse mechanism where the tubules are first to deform, followed by the thorny exterior, and finally the mesocarp layer in between. The thorns are composed of lignified bundles which run longitudinally from the base of the thorn to the tip and are embedded in softer parenchymal cells, forming a fiber reinforced composite. The mesocarp contains more lignin than any of the other layers while the core appears to contain more pectin giving rise to variations in compressive and viscoelastic properties between the layers. The surface thorns provide a compelling impact-resistant feature for bioinspiration, with a cellular structure that can withstand large deformation without failing and wavy surface features which densify during compression without fracturing. Even the conical shape of the thorns is valuable, presenting a gradually increasing surface area during axial collapse. A simplified model of this mechanism is put forward to describe the force response of these features. The thorns also distribute damage laterally during impact and deflect cracks along their interstitial valleys. These phenomena were observed in 3D printed, jackfruit-inspired designs which performed markedly better than control prints with the same mass. STATEMENT OF SIGNIFICANCE: Many biological materials have evolved remarkable structures that enhance their mechanical performance and serve as sources of inspiration for engineers. Plants are often overlooked in this regard yet certain botanical components, like nuts and fruit, have shown incredible potential as blueprints for improved impact resistant designs. The jackfruit is the largest fruit on Earth and generates significant falling impact energies. Here, we explore the jackfruit's structure and its mechanical capabilities for the first time. The progressive failure imparted by its multilayered design and the unique collapse mode of the surface thorns are identified as key mechanisms for improving the fruit's impact resistance. 3D printing is used to show that these structure-property benefits can be successfully transferred to engineering materials.

Variability of cell wall recalcitrance and composition in genotypes of Miscanthus from different genetic groups and geographical origin

Miscanthus is a promising crop for bioenergy and biorefining in Europe. The improvement of Miscanthus as a crop relies on the creation of new varieties through the hybridization of germplasm collected in the wild with genetic variation and suitable characteristics in terms of resilience, yield and quality of the biomass. Local adaptation has likely shaped genetic variation for these characteristics and is therefore important to quantify. A key biomass quality parameter for biorefining is the ease of conversion of cell wall polysaccharides to monomeric sugars. Thus far, the variability of cell wall related traits in Miscanthus has mostly been explored in accessions from limited genetic backgrounds. Here we analysed the soil and climatic conditions of the original collection sites of 592 Miscanthus genotypes, which form eight distinct genetic groups based on discriminant analysis of principal components of 25,014 single-nucleotide polymorphisms. Our results show that species of the genus Miscanthus grow naturally across a range of soil and climate conditions. Based on a detailed analysis of 49 representative genotypes, we report generally minor differences in cell wall characteristics between different genetic groups and high levels of genetic variation within groups, with less investigated species like M. floridulus showing lower recalcitrance compared to the other genetic groups. The results emphasize that both inter- and intra- specific variation in cell wall characteristics and biomass recalcitrance can be used effectively in Miscanthus breeding programmes, while also reinforcing the importance of considering biomass yield when quantifying overall conversion efficiency. Thus, in addition to reflecting the complexity of the interactions between compositional and structural cell wall features and cell wall recalcitrance to sugar release, our results point to traits that could potentially require attention in breeding programmes targeted at improving the Miscanthus biomass crop.

Lateral Root Initiation in Cucumber (Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 (RALF34) Tell Us?

In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.

Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots

The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators.

CiXTH29 and CiLEA4 Role in Water Stress Tolerance in Cichorium intybus Varieties

Drought causes massive crop quality and yield losses. Limiting the adverse effects of water deficits on crop yield is an urgent goal for a more sustainable agriculture. With this aim, six chicory varieties were subjected to drought conditions during seed germination and at the six week-old plant growth stage, in order to identify some morphological and/or molecular markers of drought resistance. Selvatica, Zuccherina di Trieste and Galatina varieties, with a high vegetative development, showed a major germination index, greater seedling development (6 days of growth) and a greater dehydration resistance (6 weeks of growth plus 10 days without water) than the other ones (Brindisina, Esportazione and Rossa Italiana). Due to the reported involvement, in the abiotic stress response, of xyloglucan endotransglucosylase/hydrolases (XTHs) and late embryogenesis abundant (LEA) multigene families, XTH29 and LEA4 expression profiles were investigated under stress conditions for all analyzed chicory varieties. We showed evidence that chicory varieties with high CiXTH29 and CiLEA4 basal expression and vegetative development levels better tolerate drought stress conditions than varieties that show overexpression of the two genes only in response to drought. Other specific morphological traits characterized almost all chicory varieties during dehydration, i.e., the appearance of lysigen cavities and a general increase of the amount of xyloglucans in the cell walls of bundle xylem vessels. Our results highlighted that high CiXTH29 and CiLEA4 basal expression, associated with a high level of vegetative growth, is a potential marker for drought stress tolerance.

Meliaceae genomes provide insights into wood development and limonoids biosynthesis

Meliaceae is a useful plant family owing to its high-quality timber and its many limonoids that have pharmacological and biological activities. Although some genomes of Meliaceae species have been reported, many questions regarding their unique family features, namely wood quality and natural products, have not been answered. In this study, we provide the whole-genome sequence of Melia azedarach comprising 237.16 Mb with a contig N50 of 8.07 Mb, and an improved genome sequence of Azadirachta indica comprising 223.66 Mb with a contig N50 of 8.91 Mb. Moreover, genome skimming data, transcriptomes and other published genomes were comprehensively analysed to determine the genes and proteins that produce superior wood and valuable limonoids. Phylogenetic analysis of chloroplast genomes, single-copy gene families and single-nucleotide polymorphisms revealed that Meliaceae should be classified into two subfamilies: Cedreloideae and Melioideae. Although the Meliaceae species did not undergo additional whole-genome duplication events, the secondary wall biosynthetic genes of the woody Cedreloideae species, Toona sinensis, expanded significantly compared to those of A. indica and M. azedarach, especially in downstream transcription factors and cellulose/hemicellulose biosynthesis-related genes. Moreover, expanded special oxidosqualene cyclase catalogues can help diversify Sapindales skeletons, and the clustered genes that regulate terpene chain elongation, cyclization and modification would support their roles in limonoid biosynthesis. The expanded clans of terpene synthase, O-methyltransferase and cytochrome P450, which are mainly derived from tandem duplication, are responsible for the different limonoid classes among the species. These results are beneficial for further investigations of wood development and limonoid biosynthesis.

An R2R3-MYB network modulates stem strength by regulating lignin biosynthesis and secondary cell wall thickening in herbaceous peony

Stem strength is an important agronomic trait affecting plant lodging, and plays an essential role in the quality and yield of plants. Thickened secondary cell walls in stems provide mechanical strength that allows plants to stand upright, but the regulatory mechanism of secondary cell wall thickening and stem strength in cut flowers remains unclear. In this study, first, a total of 11 non-redundant Paeonia lactiflora R2R3-MYBs related to stem strength were identified and isolated from cut-flower herbaceous peony, among which PlMYB43, PlMYB83 and PlMYB103 were the most upregulated differentially expressed genes. Then, the expression characteristics revealed that these three R2R3-MYBs were specifically expressed in stems and acted as transcriptional activators. Next, biological function verification showed that these P. lactiflora R2R3-MYBs positively regulated stem strength, secondary cell wall thickness and lignin deposition. Furthermore, yeast-one-hybrid and dual luciferase reporter assays demonstrated that they could bind to the promoter of caffeic acid O-methyltransferase gene (PlCOMT2) and/or laccase gene (PlLAC4), two key genes involved in lignin biosynthesis. In addition, the function of PlLAC4 in increasing lignin deposition was confirmed by virus-induced gene silencing and overexpression. Moreover, PlMYB83 could also act as a transcriptional activator of PlMYB43. The findings of the study propose a regulatory network of R2R3-MYBs modulating lignin biosynthesis and secondary cell wall thickening for improving stem lodging resistance, and provide a resource for molecular genetic engineering breeding of cut flowers.

Cell Wall Integrity Signaling in Fruit Ripening

Plant cell walls are essential structures for plant growth and development as well as plant adaptation to environmental stresses. Thus, plants have evolved signaling mechanisms to monitor the changes in the cell wall structure, triggering compensatory changes to sustain cell wall integrity (CWI). CWI signaling can be initiated in response to environmental and developmental signals. However, while environmental stress-associated CWI signaling has been extensively studied and reviewed, less attention has been paid to CWI signaling in relation to plant growth and development under normal conditions. Fleshy fruit development and ripening is a unique process in which dramatic alternations occur in cell wall architecture. Emerging evidence suggests that CWI signaling plays a pivotal role in fruit ripening. In this review, we summarize and discuss the CWI signaling in relation to fruit ripening, which will include cell wall fragment signaling, calcium signaling, and NO signaling, as well as Receptor-Like Protein Kinase (RLKs) signaling with an emphasis on the signaling of FERONIA and THESEUS, two members of RLKs that may act as potential CWI sensors in the modulation of hormonal signal origination and transduction in fruit development and ripening.