Lignin-based barrier restricts pathogens to the infection site and confers resistance in plants

Transcriptome profiling of flax plants exposed to a low-frequency alternating electromagnetic field

All living organisms on Earth evolved in the presence of an electromagnetic field (EMF), adapted to the environment of EMF, and even learned to utilize it for their purposes. However, during the last century, the Earth's core lost its exclusivity, and many EMF sources appeared due to the development of electricity and electronics. Previous research suggested that the EMF led to changes in intercellular free radical homeostasis and further altered the expression of genes involved in plant response to environmental stresses, inorganic ion transport, and cell wall constituent biosynthesis. Later, CTCT sequence motifs in gene promoters were proposed to be responsible for the response to EMF. How these motifs or different mechanisms are involved in the plant reaction to external EMF remains unknown. Moreover, as many genes activated under EMF treatment do not have the CTCT repeats in their promoters, we aimed to determine the transcription profile of a plant exposed to an EMF and identify the genes that are directly involved in response to the treatment to find the common denominator of the observed changes in the plant transcriptome.

Ethylene signals modulate the survival of Arabidopsis leaf explants

BACKGROUND

Leaf explants are major materials in plant tissue cultures. Incubation of detached leaves on phytohormone-containing media, which is an important process for producing calli and regenerating plants, change their cell fate. Although hormone signaling pathways related to cell fate transition have been widely studied, other molecular and physiological events occurring in leaf explants during this process remain largely unexplored.

RESULTS

Here, we identified that ethylene signals modulate expression of pathogen resistance genes and anthocyanin accumulation in leaf explants, affecting their survival during culture. Anthocyanins accumulated in leaf explants, but were not observed near the wound site. Ethylene signaling mutant analysis revealed that ethylene signals are active and block anthocyanin accumulation in the wound site. Moreover, expression of defense-related genes increased, particularly near the wound site, implying that ethylene induces defense responses possibly by blocking pathogenesis via wounding. We also found that anthocyanin accumulation in non-wounded regions is required for drought resistance in leaf explants.

CONCLUSIONS

Our study revealed the key roles of ethylene in the regulation of defense gene expression and anthocyanin biosynthesis in leaf explants. Our results suggest a survival strategy of detached leaves, which can be applied to improve the longevity of explants during tissue culture.

Lignin from Brewers' Spent Grain: Structural and Thermal Evaluations

Lignocellulose is a renewable ubiquitous material that comprises cellulose, hemicellulose, and lignin. Lignin has been isolated from different lignocellulosic biomass via chemical treatments, but there has been little or no investigation carried out on the processing of lignin from brewers' spent grain (BSG) to the best of authors' knowledge. This material makes up 85% of the brewery industry's byproducts. Its high moisture content hastens its deterioration, which has posed a huge challenge to its preservation and transportation; this eventually causes environmental pollution. One of the methods of solving this environmental menace is the extraction of lignin as a precursor for carbon fiber production from this waste. This study considers the viability of sourcing lignin from BSG with the use of acid solutions at 100 °C. Structural and thermal analyses were carried out on extracted samples, and the results were compared with other biomass-soured lignin to assess the proficiency of this isolation technique. Wet BSG sourced from Nigeria Breweries (NB), Lagos, was washed and sun-dried for 7 days. Tetraoxosulphate (VI) (H₂SO₄), hydrochloric (HCl), and acetic acid, each of 10 M, were individually reacted with dried BSG at 100 °C for 3 h and designated as H2, HC, and AC lignin. The residue (lignin) was washed and dried for analysis. Wavenumber shift values from Fourier transform infrared spectroscopy (FTIR) show that intra- and intermolecular OH interactions in H2 lignin are the strongest and possess the highest magnitude of hydrogen-bond enthalpy (5.73 kCal/mol). The thermogravimetric analysis (TGA) results show that a higher lignin yield can be achieved when it is isolated from BSG, as 82.9, 79.3, and 70.2% were realized for H2, HC, and AC lignin. The highest size of ordered domains (0.0299 nm) displayed by H2 lignin from X-ray diffraction (XRD) informs that it has the greatest potential of forming nanofibers via electrospinning. The enthalpy of reaction values of 133.3, 126.6, and 114.1 J/g recorded for H2, HC, and AC lignin, respectively, from differential scanning calorimetry (DSC) results affirm that H2 lignin is the most thermally stable with the highest glass transition temperature (T_g = 107 °C).

Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis

Soil salinity stress is one of the major bottlenecks for crop production. Although, allantoin is known to be involved in nitrogen metabolism in plants, yet several reports in recent time indicate its involvement in various abiotic stress responses including salinity stress. However, the detail mechanism of allantoin involvement in salinity stress tolerance in plants is not studied well. Moreover, we demonstrated the role of exogenous application of allantoin as well as increased concentration of endogenous allantoin in rendering salinity tolerance in rice and Arabidopsis respectively, via., induction of abscisic acid (ABA) and brassinosteroid (BR) biosynthesis pathways. Exogenous application of allantoin (10 µM) provides  salt-tolerance to salt-sensitive rice genotype (IR-29). Transcriptomic data after exogenous supplementation of allantoin under salinity stress showed induction of ABA (OsNCED1) and BR (Oscytochrome P450) biosynthesis genes in IR-29. Further, the key gene of allantoin biosynthesis pathway i.e., urate oxidase of the halophytic species Oryza coarctata was also found to induce ABA and BR biosynthesis genes when over-expressed in transgenic Arabidopsis. Thus, indicating that ABA and BR biosynthesis pathways were involved in allantoin mediated salinity tolerance in both rice and Arabidopsis. Additionally, it has been found that several physio-chemical parameters such as biomass, Na⁺/K⁺ ratio, MDA, soluble sugar, proline, allantoin and chlorophyll contents were also associated with the allantoin-mediated salinity tolerance in urate oxidase overexpressed lines of Arabidopsis. These findings depicted the functional conservation of allantoin for salinity tolerance in both plant clades.

OsNPR1 Enhances Rice Resistance to Xanthomonas oryzae pv. oryzae by Upregulating Rice Defense Genes and Repressing Bacteria Virulence Genes

The bacteria pathogen Xanthomonas oryzae pv. oryzae (Xoo) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression of OsNPR1 significantly increases rice resistance to Xoo. Although some downstream rice genes were found to be regulated by OsNPR1, how OsNPR1 affects the interaction of rice-Xoo and alters Xoo gene expression remains unknown. In this study, we challenged the wild-type and OsNPR1-OE rice materials with Xoo and performed dual RNA-seq analyses for the rice and Xoo genomes simultaneously. In Xoo-infected OsNPR1-OE plants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand, Xoo genes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes of Xoo, including genes encoding components of type III and other secretion systems, were downregulated by OsNPR1 overexpression. Our results suggest that OsNPR1 enhances rice resistance to Xoo by bidirectionally regulating gene expression in rice and Xoo.

Stigma type and transcriptome analyses of mulberry revealed the key factors associated with Ciboria shiraiana resistance

Ciboria shiraiana is a fungal pathogen and the causal agent of hypertrophy sorosis scleroteniosis (HSS) in mulberry, leading to substantial economic losses in the mulberry fruit-related industry. To obtain HSS resistant resources and investigate the resistance mechanism, the resistances of 14 mulberry varieties were assessed. Morus laevigata Wall. (MLW) varieties showed strong resistance to C. shiraiana, and the pathogen's infection was associated with mulberry fluorescence. Stigmas were identified as the infection site through cutting experiments. Susceptible varieties (S-varieties) displayed secretory droplets on their stigma papillar cell surfaces, while MLWs lacked these secretions. Correlation analysis between the secretion rate and the diseased fruit rate indicated that the differences between resistant varieties (R-varieties) and S-varieties were related to the stigma type. Furthermore, comparative transcriptome analysis was performed on stigma and ovary samples from R- and S-varieties. Compared with the stigma of R-varieties, the key differentially expressed genes (DEGs) with significantly higher expression in S-variety stigmas mainly participated in the fatty acid biosynthetic process. In R-variety stigmas and ovaries, the transcript levels of DEGs involved in defense response, including resistance (R) genes, were significantly higher than that of S-varieties. Overexpression of MlwRPM1-2 and MlwRGA3 enhances resistance to C. shiraiana and Sclerotinia sclerotiorum, but not Botrytis cinerea in tobacco. These findings help us explain the different resistance mechanisms of mulberry to C. shiraiana, and the critical defense genes in R-varieties can be applied to breeding antifungal plant varieties.

Injectable Antioxidant and Oxygen-Releasing Lignin Composites to Promote Wound Healing

The application of engineered biomaterials for wound healing has been pursued since the beginning of tissue engineering. Here, we attempt to apply functionalized lignin to confer antioxidation to the extracellular microenvironments of wounds and to deliver oxygen from the dissociation of calcium peroxide for enhanced vascularization and healing responses without eliciting inflammatory responses. Elemental analysis showed 17 times higher quantity of calcium in the oxygen-releasing nanoparticles. Lignin composites including the oxygen-generating nanoparticles released around 700 ppm oxygen per day at least for 7 days. By modulating the concentration of the methacrylated gelatin, we were able to maintain the injectability of lignin composite precursors and the stiffness of lignin composites suitable for wound healing after photo-cross-linking. In situ formation of lignin composites with the oxygen-releasing nanoparticles enhanced the rate of tissue granulation, the formation of blood vessels, and the infiltration of α-smooth muscle actin⁺ fibroblasts into the wounds over 7 days. At 28 days after surgery, the lignin composite with oxygen-generating nanoparticles remodeled the collagen architecture, resembling the basket-weave pattern of unwounded collagen with minimal scar formation. Thus, our study shows the potential of functionalized lignin for wound-healing applications requiring balanced antioxidation and controlled release of oxygen for enhanced tissue granulation, vascularization, and maturation of collagen.

Host Resistance to Parasitic Plants-Current Knowledge and Future Perspectives

Parasitic flowering plants represent a diverse group of angiosperms, ranging from exotic species with limited distribution to prominent weeds, causing significant yield losses in agricultural crops. The major damage caused by them is related to the extraction of water and nutrients from the host, thus decreasing vegetative growth, flowering, and seed production. Members of the root parasites of the Orobanchaceae family and stem parasites of the genus Cuscuta are among the most aggressive and damaging weeds, affecting both monocotyledonous and dicotyledonous crops worldwide. Their control and eradication are hampered by the extreme seed longevity and persistence in soil, as well as their taxonomic position, which makes it difficult to apply selective herbicides not damaging to the hosts. The selection of resistant cultivars is among the most promising approaches to deal with this matter, although still not widely employed due to limited knowledge of the molecular mechanisms of host resistance and inheritance. The current review aims to summarize the available information on host resistance with a focus on agriculturally important parasitic plants and to outline the future perspectives of resistant crop cultivar selection to battle the global threat of parasitic plants.

CcNAC1 by Transcriptome Analysis Is Involved in Sudan Grass Secondary Cell Wall Formation as a Positive Regulator

Sudan grass is a high-quality forage of sorghum. The degree of lignification of Sudan grass is the main factor affecting its digestibility in ruminants such as cattle and sheep. Almost all lignocellulose in Sudan grass is stored in the secondary cell wall, but the mechanism and synthesis of the secondary cell wall in Sudan grass is still unclear. In order to study the mechanism of secondary cell wall synthesis in Sudan grass, we used an in vitro induction system of Sudan grass secondary cell wall. Through transcriptome sequencing, it was found that the NAC transcription factor CcNAC1 gene was related to the synthesis of the Sudan grass secondary cell wall. This study further generated CcNAC1 overexpression lines of Arabidopsis to study CcNAC1 gene function in secondary cell wall synthesis. It was shown that the overexpression of the CcNAC1 gene can significantly increase lignin content in Arabidopsis lines. Through subcellular localization analysis, CcNAC1 genes could be expressed in the nucleus of a plant. In addition, we used yeast two-hybrid screening to find 26 proteins interacting with CcNAC1. GO and KEGG analysis showed that CcNAC1 relates to the metabolic pathways and biosynthesis of secondary metabolites. In summary, the synthesis of secondary cell wall of Sudan grass can be regulated by CcNAC1.

Directed growth and fusion of membrane-wall microdomains requires CASP-mediated inhibition and displacement of secretory foci

Casparian strips (CS) are aligned bands of lignin-impregnated cell walls, building an extracellular diffusion barrier in roots. Their structure profoundly differs from tight junctions (TJ), analogous structures in animals. Nonetheless, CS membrane domain (CSD) proteins 1-5 (CASP1-5) are homologues of occludins, TJ components. CASP-marked membranes display cell wall (matrix) adhesion and membrane protein exclusion. A full CASP knock-out now reveals CASPs are not needed for localized lignification, since correctly positioned lignin microdomains still form in the mutant. Ultra-structurally, however, these microdomains are disorganized, showing excessive cell wall growth, lack of exclusion zone and matrix adhesion, and impaired exocyst dynamics. Proximity-labelling identifies a Rab-GTPase subfamily, known exocyst activators, as potential CASP-interactors and demonstrate their localization and function at the CSD. We propose that CASP microdomains displace initial secretory foci by excluding vesicle tethering factors, thereby ensuring rapid fusion of microdomains into a membrane-cell wall band that seals the extracellular space.

The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility

Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase (PAL), the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaβLIM1a by interfering with its DNA-binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.

Untargeted profiling of secondary metabolites and phytotoxins associated with stemphylium blight of lentil

Stemphylium botryosum alters lentil secondary metabolism and differentially affects resistant and susceptible genotypes. Untargeted metabolomics identifies metabolites and their potential biosynthetic pathways that play a crucial role in resistance to S. botryosum. The molecular and metabolic processes that mediate resistance to stemphylium blight caused by Stemphylium botryosum Wallr. in lentil are largely unknown. Identifying metabolites and pathways associated with Stemphylium infection may provide valuable insights and novel targets to breed for enhanced resistance. The metabolic changes following infection of four lentil genotypes by S. botryosum were investigated by comprehensive untargeted metabolic profiling employing reversed-phase or hydrophilic interaction liquid chromatography (HILIC) coupled to a Q-Exactive mass spectrometer. At the pre-flowering stage, plants were inoculated with S. botryosum isolate SB19 spore suspension and leaf samples were collected at 24, 96 and 144 h post-inoculation (hpi). Mock-inoculated plants were used as negative controls. After analyte separation, high-resolution mass spectrometry data was acquired in positive and negative ionization modes. Multivariate modeling revealed significant treatment, genotype and hpi effects on metabolic profile changes that reflect lentil response to Stemphylium infection. In addition, univariate analyses highlighted numerous differentially accumulated metabolites. By contrasting the metabolic profiles of SB19-inoculated and mock-inoculated plants and among lentil genotypes, 840 pathogenesis-related metabolites were detected including seven S. botryosum phytotoxins. These metabolites included amino acids, sugars, fatty acids and flavonoids in primary and secondary metabolism. Metabolic pathway analysis revealed 11 significant pathways including flavonoid and phenylpropanoid biosynthesis, which were affected upon S. botryosum infection. This research contributes to ongoing efforts toward a comprehensive understanding of the regulation and reprogramming of lentil metabolism under biotic stress, which will provide targets for potential applications in breeding for enhanced disease resistance.

Brown midrib mutant and genome-wide association analysis uncover lignin genes for disease resistance in maize

Brown midrib (BMR) maize (Zea mays L.) harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate New York highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3, and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot [GLS], and anthracnose leaf blight [ALB]) and bacterial (Stewart's wilt) diseases. The bm1, bm2, and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot (ASR), and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot (GER). Colocalization of quantitative trait loci (QTL) and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered single-nucleotide polymorphism (SNP) associations for resistance to NLB but did not implicate natural functional variation at bm1-bm5. Strong associations implicated a suite of diverse candidate genes including lignin-related genes such as a β-glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP-like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and nonsilage purposes.

Molecular module of CmMYB15-like-Cm4CL2 regulating lignin biosynthesis of chrysanthemum (Chrysanthemum morifolium) in response to aphid (Macrosiphoniella sanborni) feeding

Lignin is a major component of plant cell walls and a conserved basic defense mechanism in higher plants deposited in response to aphid infection. However, the molecular mechanisms of lignin biosynthesis in response to aphid infection and the effect of lignin on aphid feeding behavior remain unclear. We report that 4-Coumarate:coenzyme A ligase 2 (Cm4CL2), a gene encoding a key enzyme in the lignin biosynthesis pathway, is induced by aphid feeding, resulting in lignin deposition and reduced aphid attack. Upstream regulator analysis showed that the expression of Cm4CL2 in response to aphid feeding was directly upregulated by CmMYB15-like, an SG2-type R2R3-MYB transcription factor. CmMYB15-like binds directly to the AC cis-element in the promoter region of Cm4CL2. Genetic validation demonstrated that CmMYB15-like was induced by aphid infection and contributed to lignin deposition and cell wall thickening, which consequently enhanced aphid resistance in a Cm4CL2-dependent manner. This study is the first to show that the CmMYB15-like-Cm4CL2 module regulates lignin biosynthesis in response to aphid feeding.

Effects of a Pseudomonas Strain on the Lipid Transfer Proteins, Appoplast Barriers and Activity of Aquaporins Associated with Hydraulic Conductance of Pea Plants

Lipid transfer proteins (LTPs) are known to be involved in suberin deposition in the Casparian bands of pea roots, thereby reinforcing apoplast barriers. Moreover, the Pseudomonas mandelii IB-Ki14 strain accelerated formation of the Casparian bands in wheat plants, although involvement of LTPs in the process was not studied. Here, we investigated the effects of P. mandelii IB-Ki14 on LTPs, formation of the Casparian bands, hydraulic conductance and activity of aquaporins (AQPs) in pea plants. RT PCR showed a 1.6-1.9-fold up-regulation of the PsLTP-coding genes and an increase in the abundance of LTP proteins in the phloem of pea roots induced by the treatment with P. mandelii IB-Ki14. The treatment was accompanied with increased deposition of suberin in the Casparian bands. Hydraulic conductance did not decrease in association with the bacterial treatment despite strengthening of the apoplast barriers. At the same time, the Fenton reagent, serving as an AQPs inhibitor, decreased hydraulic conductance to a greater extent in treated plants relative to the control group, indicating an increase in the AQP activity by the bacteria. We hypothesize that P. mandelii IB-Ki14 stimulates deposition of suberin, in the biosynthesis of which LTPs are involved, and increases aquaporin activity, which in turn prevents a decrease in hydraulic conductance due to formation of the apoplast barriers in pea roots.

High value valorization of lignin as environmental benign antimicrobial

Lignin is a natural aromatic polymer of p-hydroxyphenylpropanoids with various biological activities. Noticeably, plants have made use of lignin as biocides to defend themselves from pathogen microbial invasions. Thus, the use of isolated lignin as environmentally benign antimicrobial is believed to be a promising high value approach for lignin valorization. On the other hand, as green and sustainable product of plant photosynthesis, lignin should be beneficial to reduce the carbon footprint of antimicrobial industry. There have been many reports that make use of lignin to prepare antimicrobials for different applications. However, lignin is highly heterogeneous polymers different in their monomers, linkages, molecular weight, and functional groups. The structure and property relationship, and the mechanism of action of lignin as antimicrobial remains ambiguous. To show light on these issues, we reviewed the publications on lignin chemistry, antimicrobial activity of lignin models and isolated lignin and associated mechanism of actions, approaches in synthesis of lignin with improved antimicrobial activity, and the applications of lignin as antimicrobial in different fields. Hopefully, this review will help and inspire researchers in the preparation of lignin antimicrobial for their applications.

Pathogen-induced autophagy regulates monolignol transport and lignin formation in plant immunity

The evolutionary plant-pathogen arms race has equipped plants with the immune system that can defend against pathogens. Pattern-triggered immunity and effector-triggered immunity are two major branches of innate immunity that share immune responses, including oxidative bursts, transcriptional reprogramming, and cell wall modifications such as lignin deposition. In a previous study, we reported that lignin rapidly accumulates in pathogen-infected Arabidopsis leaves and acts as a mechanical barrier, spatially restricting pathogens and cell death. Lignin deposition into the cell wall is a three-step process: monolignol biosynthesis, transport, and polymerization. While monolignol biosynthesis and polymerization are relatively well understood, the mechanism of monolignol transport remains unclear. In this study, we show that macroautophagy/autophagy modulates pathogen-induced lignin formation. Lignification and other immune responses were impaired in autophagy-defective atg (autophagy-related) mutants. In microscopy analyses, monolignols formed punctate structures in response to pathogen infection and colocalized with autophagic vesicles. Furthermore, autophagic activity and lignin accumulation were both enhanced in dnd1 (defense, no death 1) mutant with elevated disease resistance but no cell death and crossing dnd1-1 with atg mutants resulted in a lignin deficit, further supporting that lignin formation requires autophagy. Collectively, these findings demonstrate that lignification, particularly monolignol transport, is achieved through autophagic membrane trafficking in plant immunity.Abbreviations: ABC transporter: ATP-binding cassette transporter; ACD2/AT4G37000: accelerated cell death 2; ATG: autophagy-related; C3'H/AT2G40890: p-coumaroyl shikimate 3-hydroxylase; C4H/AT2G30490: cinnamate 4-hydroxylase; CA: coniferyl alcohol; CaMV: cauliflower mosaic virus; CASP: Casparian strip membrane domain protein; CASPL: CASP-like protein; CBB: Coomassie Brilliant Blue; CCoAOMT1/AT4G34050: caffeoyl-CoA O-methyltransferase 1; CCR1/AT1G15950: cinnamoyl-CoA reductase 1; CFU: colony-forming unit; COMT1/AT5G54160: caffeic acid O-methyltransferase 1; Con A: concanamycin A; DMAC: dimethylaminocoumarin; DND1/AT5G15410: defense, no death 1; CNGC2: cyclic nucleotide-gated channel 2; ER: endoplasmic reticulum; ESB1/AT2G28670/DIR10: enhanced suberin 1; ETI: effector-triggered immunity; EV: extracellular vesicle; F5H/AT4G36220: ferulate-5-hydroxylase; Fluo-3 AM: Fluo-3 acetoxymethyl ester; GFP: green fluorescent protein; HCT/AT5G48930: p-hydroxycinnamoyl-CoA:quinate/shikimate p-hydroxycinnamoyltransferase; HR: hypersensitive response; LAC: laccase; LTG: LysoTracker Green; LSD1/AT4G200380: lesion stimulating disease 1; PAL1/AT2G37040: phenylalanine ammonia-lyase 1; PAMP: pathogen-associated molecular patterns; PCD: programmed cell death; PE: phosphatidylethanolamine; PRX: peroxidase; Pst DC3000: Pseudomonas syringe pv. tomato DC3000; PTI: pattern-triggered immunity; SA: salicylic acid; SD: standard deviation; SID2/AT1G7410: SA induction-deficient 2; UGT: UDP-glucosyltransferase; UPLC: ultraperformance liquid chromatography; UPS: unconventional protein secretion; V-ATPase: vacuolar-type H⁺-translocating ATPase.

Quantitative disease resistance: Multifaceted players in plant defense

In contrast to large-effect qualitative disease resistance, quantitative disease resistance (QDR) exhibits partial and generally durable resistance and has been extensively utilized in crop breeding. The molecular mechanisms underlying QDR remain largely unknown but considerable progress has been made in this area in recent years. In this review, we summarize the genes that have been associated with plant QDR and their biological functions. Many QDR genes belong to the canonical resistance gene categories with predicted functions in pathogen perception, signal transduction, phytohormone homeostasis, metabolite transport and biosynthesis, and epigenetic regulation. However, other "atypical" QDR genes are predicted to be involved in processes that are not commonly associated with disease resistance, such as vesicle trafficking, molecular chaperones, and others. This diversity of function for QDR genes contrasts with qualitative resistance, which is often based on the actions of nucleotide-binding leucine-rich repeat (NLR) resistance proteins. An understanding of the diversity of QDR mechanisms and of which mechanisms are effective against which classes of pathogens will enable the more effective deployment of QDR to produce more durably resistant, resilient crops.

Crossroads in the evolution of plant specialized metabolism

The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.

Genomic and metabolic profiling of two tomato contrasting cultivars for tolerance to Tuta absoluta

Dissimilar patterns of variants affecting genes involved in response to herbivory, including those leading to difference in VOC production, were identified in tomato lines with contrasting response to Tuta absoluta. Tuta absoluta is one of the most destructive insect pest affecting tomato production, causing important yield losses both in open field and greenhouse. The selection of tolerant varieties to T. absoluta is one of the sustainable approaches to control this invasive leafminer. In this study, the genomic diversity of two tomato varieties, one tolerant and the other susceptible to T. absoluta infestation was explored, allowing us to identify chromosome regions with highly dissimilar pattern. Genes affected by potential functional variants were involved in several processes, including response to herbivory and secondary metabolism. A metabolic analysis for volatile organic compounds (VOCs) was also performed, highlighting a difference in several classes of chemicals in the two genotypes. Taken together, these findings can aid tomato breeding programs aiming to develop tolerant plants to T. absoluta.

Induced defense strategies of plants against Ralstonia solanacearum

Plants respond to Ralstonia solanacearum infestation through two layers of immune system (PTI and ETI). This process involves the production of plant-induced resistance. Strategies for inducing resistance in plants include the formation of tyloses, gels, and callose and changes in the content of cell wall components such as cellulose, hemicellulose, pectin, lignin, and suberin in response to pathogen infestation. When R. solanacearum secrete cell wall degrading enzymes, plants also sense the status of cell wall fragments through the cell wall integrity (CWI) system, which activates deep-seated defense responses. In addition, plants also fight against R. solanacearum infestation by regulating the distribution of metabolic networks to increase the production of resistant metabolites and reduce the production of metabolites that are easily exploited by R. solanacearum. We review the strategies used by plants to induce resistance in response to R. solanacearum infestation. In particular, we highlight the importance of plant-induced physical and chemical defenses as well as cell wall defenses in the fight against R. solanacearum.

MePAL6 regulates lignin accumulation to shape cassava resistance against two-spotted spider mite

INTRODUCTION

The two-spotted spider mite (TSSM) is a devastating pest of cassava production in China. Lignin is considered as an important defensive barrier against pests and diseases, several genes participate in lignin biosynthesis, however, how these genes modulate lignin accumulation in cassava and shape TSSM-resistance is largely unknown.

METHODS

To fill this knowledge gap, while under TSSM infestation, the cassava lignin biosynthesis related genes were subjected to expression pattern analysis followed by family identification, and genes with significant induction were used for further function exploration.

RESULTS

Most genes involved in lignin biosynthesis were up-regulated when the mite-resistant cassava cultivars were infested by TSSM, noticeably, the MePAL gene presented the most vigorous induction among these genes. Therefore, we paid more attention to dissect the function of MePAL gene during cassava-TSSM interaction. Gene family identification showed that there are 6 MePAL members identified in cassava genome, further phylogenetic analysis, gene duplication, cis-elements and conserved motif prediction speculated that these genes may probably contribute to biotic stress responses in cassava. The transcription profile of the 6 MePAL genes in TSSM-resistant cassava cultivar SC9 indicated a universal up-regulation pattern. To further elucidate the potential correlation between MePAL expression and TSSM-resistance, the most strongly induced gene MePAL6 were silenced using virus-induced gene silencing (VIGS) assay, we found that silencing of MePAL6 in SC9 not only simultaneously suppressed the expression of other lignin biosynthesis genes such as 4-coumarate--CoA ligase (4CL), hydroxycinnamoyltransferase (HCT) and cinnamoyl-CoA reductase (CCR), but also resulted in decrease of lignin content. Ultimately, the suppression of MePAL6 in SC9 can lead to significant deterioration of TSSM-resistance.

DISCUSSION

This study accurately identified MePAL6 as critical genes in conferring cassava resistance to TSSM, which could be considered as promising marker gene for evaluating cassava resistance to insect pest.

Secretory membrane traffic in plant-microbe interactions

Plant defense responses include the extracellular release of defense-related molecules, such as pathogenesis-related proteins and secondary metabolites, as well as cell wall materials. This primarily depends on the trafficking of secretory vesicles to the plasma membrane, where they discharge their contents into the apoplastic space via soluble N-ethylmaleimide sensitive factor attachment protein receptor-assisted exocytosis. However, some pathogenic and symbiotic microbes have developed strategies to manipulate host plant exocytic pathways. Here, we discuss the mechanisms by which plant exocytic pathways function in immunity and how microbes have evolved to manipulate those pathways.

Differential Colonization of the Plant Vasculature Between Endophytic Versus Pathogenic Fusarium oxysporum Strains

Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains in Arabidopsis thaliana and Solanum lycopersicum, using Arabidopsis pathogen Fo5176, tomato pathogen Fol4287, and the endophyte Fo47, which can colonize both plant hosts. We observed that all strains were able to advance from epidermis to endodermis within 3 days postinoculation (dpi) and reached the root xylem at 4 dpi. However, this shared progression was restricted to lateral roots and the elongation zone of the primary root. Only pathogens reached the xylem above the primary-root maturation zone (PMZ). Related to the distinct colonization patterns, we also observed stronger induction of callose at the PMZ and lignin deposition at primary-lateral root junctions by the endophyte in both plants. This observation was further supported by stronger induction of Arabidopsis genes involved in callose and lignin biosynthesis during the endophytic colonization (Fo47) compared with the pathogenic interaction (Fo5176). Moreover, both pathogens encode more plant cell wall-degrading enzymes than the endophyte Fo47. Therefore, observed differences in callose and lignin deposition could be the combination of host production and the subsequent fungal degradation. In summary, this study demonstrates spatial differences between endophytic and pathogenic colonization, strongly suggesting that further investigations of molecular arm-races are needed to understand how plants differentiate friend from foe. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Modulation of lignin biosynthesis for drought tolerance in plants

Lignin is a complex polymer that is embedded in plant cell walls to provide physical support and water protection. For these reasons, the production of lignin is closely linked with plant adaptation to terrestrial regions. In response to developmental cues and external environmental conditions, plants use an elaborate regulatory network to determine the timing and location of lignin biosynthesis. In this review, we summarize the canonical lignin biosynthetic pathway and transcriptional regulatory network of lignin biosynthesis, consisting of NAC and MYB transcription factors, to explain how plants regulate lignin deposition under drought stress. Moreover, we discuss how the transcriptional network can be applied to the development of drought tolerant plants.

Biorefining waste into nanobiotechnologies can revolutionize sustainable agriculture

Modern agriculture has evolved technological innovations to sustain crop productivity. Recent advances in biorefinery technology use crop residue as feedstock, but this raises carbon sequestration concerns as biorefining utilizes carbon that would otherwise be returned to the soil, thus causing a decline in crop productivity. Furthermore, biorefining generates abundant lignin waste that significantly impedes the efficiency of biorefineries. Valorizing lignin into advanced nanobiotechnologies for agriculture provides a unique opportunity to balance bioeconomy and soil carbon sequestration. Integration of agricultural practices such as utilization of agrochemicals, fertilizers, soil modifiers, and mulching with lignin nanobiotechnologies promotes crop productivity and also enables advanced manufacturing of high-value bioproducts from lignin. Lignin nanobiotechnologies thus represent state-of-the-art innovations to transform both the bioeconomy and sustainable agriculture.

The barley DIR gene family: An expanded gene family that is involved in stress responses

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.

Antibacterial lignin-based nanoparticles and their use in composite materials

Lignin, one of the most abundant biopolymers on earth, has been traditionally considered a low-value by-product of the pulp and paper industries. This renewable raw material, besides being a source of valuable molecules for the chemical industry, also has antioxidant, UV-absorbing, and antibacterial properties in its macromolecular form. Moreover, lignin in the form of nanoparticles (LigNPs) presents advantages over bulk lignin, such as higher reactivity due to its larger surface-to-volume ratio. In view of the rapid surge of antimicrobial resistance (AMR), caused by the overuse of antibiotics, continuous development of novel antibacterial agents is needed. The use of LigNPs as antibacterial agents is a suitable alternative to conventional antibiotics for topical application or chemical disinfectants for surfaces and packaging. Besides, their multiple and unspecific targets in the bacterial cell may prevent the emergence of AMR. This review summarizes the latest developments in antibacterial nano-formulated lignin, both in dispersion and embedded in materials. The following roles of lignin in the formulation of antibacterial NPs have been analyzed: (i) an antibacterial active in nanoformulations, (ii) a reducing and capping agent for antimicrobial metals, and (iii) a carrier of other antibacterial agents. Finally, the review covers the inclusion of LigNPs in films, fibers, hydrogels, and foams, for obtaining antibacterial lignin-based nanocomposites for a variety of applications, including food packaging, wound healing, and medical coatings.

Transcriptional Reactivation of Lignin Biosynthesis for the Heterologous Production of Etoposide Aglycone in Nicotiana benthamiana

Nicotiana benthamiana is a valuable plant chassis for heterologous production of medicinal plant natural products. This host is well suited for the processing of organelle-localized plant enzymes, and the conservation of the primary metabolism across the plant kingdom often provides required plant-specific precursor molecules that feed a given pathway. Despite this commonality in metabolism, limited precursor supply and/or competing host pathways can interfere with yields of heterologous products. Here, we use transient transcriptional reprogramming of endogenous N. benthamiana metabolism to drastically improve flux through the etoposide pathway derived from the medicinal plant Podophyllum spp. Specifically, coexpression of a single lignin-associated transcription factor, MYB85, with pathway genes results in unprecedented levels of heterologous product accumulation in N. benthamiana leaves: 1 mg/g dry weight (DW) of the etoposide aglycone, 35 mg/g DW (-)-deoxypodophyllotoxin, and 3.5 mg/g DW (-)-epipodophyllotoxin─up to two orders of magnitude above previously reported biosynthetic yields for the etoposide aglycone and eight times higher than what is observed for (-)-deoxypodophyllotoxin in the native medicinal plant. Unexpectedly, transient activation of lignin metabolism by transcription factor overexpression also reduces the production of undesired side products that likely result from competing N. benthamiana metabolism. Our work demonstrates that synthetic activation of lignin biosynthesis in leaf tissue is an effective strategy for optimizing the production of medicinal compounds derived from phenylpropanoid precursors in the plant chassis N. benthamiana. Furthermore, our results highlight the engineering value of MYB85, an early switch in lignin biosynthesis, for on-demand modulation of monolignol flux and support the role of MYB46 as a master regulator of lignin polymer deposition.

Characterization of infected process and primary mechanism in rice Acuce defense against rice blast fungus, Magnaporthe oryzae

Identification of infection process and defense response during M. oryzae infecting Acuce. Magnaporthe oryzae is a destructive rice pathogen. Recent studies have focused on the initial infectious stage, with a few studies conducted to elucidate the characteristics of the late infectious stages. This study aims to decipher the characteristics at different stages (biotrophic, biotrophy-necrotrophy switch (BNS), and necrotrophic) between the interaction of two M. oryzae-rice combinations and investigate the resistance mechanisms of rice to M. oryzae using cytological and molecular methods. The biotrophic phase of M. oryzae-LTH compatible interaction was found to be longer than that of M. oryzae-Acuce incompatible interaction. We also found that jasmonic acid (JA) signaling plays an important role in defense by regulating antimicrobial compound accumulation in infected Acuce via a synergistic interaction of JA-salicylic acid (SA) and JA-ethylene (ET). In infected LTH, JA-ET/JA-SA showed antagonistic interaction. Ibuprofen (IBU) is a JA inhibitor. Despite the above findings, we found that exogenous JA-Ile and IBU significantly alleviated blast symptoms in infected LTH at 36 hpi (biotrophic) and 72 hpi (BNS), indicating these two-time points may be critical for managing blast disease in the compatible interaction. Conversely, IBU significantly increased blast symptoms on the infected Acuce at 36 hpi, confirming that the JA signal plays a central role in the defense response in infected Acuce. According to transcriptional analysis, the number of genes enriched in the plant hormone signal pathway was significantly higher than in other pathways. Our findings suggested that JA-mediated defense mechanism is essential in regulating Acuce resistance, particularly during the biotrophic and BNS phases.

Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects

A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.

Identification of novel genetic regions associated with resistance to European canker in apple

BACKGROUND

European canker, caused by the fungal pathogen Neonectria ditissima, is an economically damaging disease in apple producing regions of the world - especially in areas with moderate temperatures and high rainfall. The pathogen has a wide host range of hardwood perennial species, causing trunk cankers, dieback and branch lesions in its hosts. Although apple scion germplasm carrying partial resistance to the disease has been described, little is still known of the genetic basis for this quantitative resistance.

RESULTS

Resistance to Neonectria ditissima was studied in a multiparental population of apple scions using several phenotyping methods. The studied population consists of individuals from multiple families connected through a common pedigree. The degree of disease of each individual in the population was assessed in three experiments: artificial inoculations of detached dormant shoots, potted trees in a glasshouse and in a replicated field experiment. The genetic basis of the differences in disease was studied using a pedigree-based analysis (PBA). Three quantitative trait loci (QTL), on linkage groups (LG) 6, 8 and 10 were identified in more than one of the phenotyping strategies. An additional four QTL, on LG 2, 5, 15 and 16 were only identified in the field experiment. The QTL on LG2 and 16 were further validated in a biparental population. QTL effect sizes were small to moderate with 4.3 to 19% of variance explained by a single QTL. A subsequent analysis of QTL haplotypes revealed a dynamic response to this disease, in which the estimated effect of a haplotype varied over the field time-points.

CONCLUSIONS

This study describes the first identified QTL associated with resistance to N. ditissima in apple scion germplasm. The results from this study show that QTL present in germplasm commonly used in apple breeding have a low to medium effect on resistance to N. ditissima. Hence, multiple QTL will need to be considered to improve resistance through breeding.

Adaptive strategies of Scots pine under shade: Increase in lignin synthesis and ecotypic variation in defense-related gene expression

Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growing season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defense-related genes (growth-defense trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defense-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.

Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in Norway spruce

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots

While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.

Development and diversity of lignin patterns

Different patterns of lignified cell walls are associated with diverse functions in a variety of plant tissues. These functions rely on the stiffness and hydrophobicity that lignin polymers impart to the cell wall. The precise pattern of subcellular lignin deposition is critical for the structure-function relationship in each lignified cell type. Here, we describe the role of xylem vessels as water pipes, Casparian strips as apoplastic barriers, and the role of asymmetrically lignified endocarp b cells in exploding seed pods. We highlight similarities and differences in the genetic mechanisms underpinning local lignin deposition in these diverse cell types. By bringing together examples from different developmental contexts and different plant species, we propose that comparative approaches can benefit our understanding of lignin patterning mechanisms.

Integrated transcriptomic and transgenic analyses reveal potential mechanisms of poplar resistance to Alternaria alternata infection

BACKGROUND

Populus davidiana × P. bollena is a species of poplar from northeastern China that is characterized by cold resistance and fast growth but now suffers from pathogen infections. Leaf blight caused by Alternaria alternata has become a common poplar disease that causes serious economic impacts, but the molecular mechanisms of resistance to A. alternata in P. davidiana × P. bollena are still unclear.

RESULTS

In this study, the transcriptomic response of P. davidiana × P. bollena to A. alternata infection was determined via RNA-Seq. Twelve cDNA libraries were generated from RNA isolated from three biological replicates at four time points (0, 2, 3, and 4 d post inoculation), and a total of 5,930 differentially expressed genes (DEGs) were detected (| log2 fold change |≥ 1 and FDR values < 0.05). Functional analysis revealed that the DEGs were mainly enriched for the "plant hormone signal transduction" pathway, followed by the "phenylpropanoid biosynthesis" pathway. In addition, DEGs that encode defense-related proteins and are related to ROS metabolism were also identified. Numerous transcription factors, such as the bHLH, WRKY and MYB families, were also induced by A. alternata infection. Among these DEGs, those related to JA biosynthesis and JA signal transduction were consistently activated. Therefore, the lipoxygenase gene PdbLOX2, which is involved in JA biosynthesis, was selected for functional characterization. Overexpression of PdbLOX2 enhanced the resistance of P. davidiana × P. bollena to A. alternata, whereas silencing this gene enhanced susceptibility to A. alternata infection.

CONCLUSIONS

These results provide new insight into the molecular mechanisms of poplar resistance to A. alternata infection and provide candidate genes for breeding resistant cultivars using genetic engineering.

Ca2+ mediates transcription factor PuDof2.5 and suppresses stone cell production in pear fruits

Stone cells are sclerenchyma cells formed by deposition of lignin, which is the most significant factor limiting the quality of pears. Ca²⁺ was known to inhibit stone cells in pear fruits, but the underlying molecular mechanism remains unclear. Our study revealed that exogenous CaCl₂ (Ca²⁺) treatment of "Nanguo" pear (Pyrus ussuriensis) suppressed the synthesis of lignin and stone cell production. We further analysed the transcriptomes using RNA-seq, identified a transcription factor, PuDof2.5, and its targets gene PuPRX42-like (lignin polymerase gene) expression decreased in CaCl₂-treated samples, which are involved in suppressing lignin biosynthesis in pear fruit. PuDof2.5 was found to bind directly to the PuPRX42-like promoter and induced its transcription. Taken together, our results revealed that Ca²⁺ modulated the key lignin biosynthetic transcription factor PuDof2.5 to suppress stone cell production in pear fruits.

Temperature- and light stress adaptations in Zygnematophyceae: The challenges of a semi-terrestrial lifestyle

Streptophyte green algae comprise the origin of land plants and therefore life on earth as we know it today. While terrestrialization opened new habitats, leaving the aquatic environment brought additional abiotic stresses. More-drastic temperature shifts and high light levels are major abiotic stresses in semi-terrestrial habitats, in addition to desiccation, which has been reviewed elsewhere. Zygnematophyceae, a species-rich class of streptophyte green algae, is considered a sister-group to embryophytes. They have developed a variety of avoidance and adaptation mechanisms to protect against temperature extremes and high radiation in the form of photosynthetically active and ultraviolet radiation (UV) radiation occurring on land. Recently, knowledge of transcriptomic and metabolomic changes as consequences of these stresses has become available. Land-plant stress-signaling pathways producing homologs of key enzymes have been described in Zygnematophyceae. An efficient adaptation strategy is their mat-like growth habit, which provides self-shading and protects lower layers from harmful radiation. Additionally, Zygnematophyceae possess phenolic compounds with UV-screening ability. Resting stages such as vegetative pre-akinetes tolerate freezing to a much higher extent than do young cells. Sexual reproduction occurs by conjugation without the formation of flagellated male gametes, which can be seen as an advantage in water-deficient habitats. The resulting zygospores possess a multilayer cell wall, contributing to their resistance to terrestrial conditions. Especially in the context of global change, understanding temperature and light tolerance is crucial.

Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm

Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03208-0.

Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease

Western hemlock (Tsuga heterophylla) is highly susceptible to Annosus root and butt rot disease, caused by Heterobasidion occidentale across its native range in western North America. Understanding molecular mechanisms of tree defense and dissecting genetic components underlying disease resistance will facilitate forest breeding and disease control management. The aim of this study was to profile host transcriptome reprogramming in response to pathogen infection using RNA-seq analysis. Inoculated seedlings were clearly grouped into three types: quantitative resistant (QR), susceptible (Sus), and un-infected (Uif), based on profiles of H. occidentale genes expressed in host tissues. Following de novo assembly of a western hemlock reference transcriptome with more than 33,000 expressed genes, the defensive transcriptome reprogramming was characterized and a set of differentially expressed genes (DEGs) were identified with gene ontology (GO) annotation. The QR seedlings showed controlled and coordinated molecular defenses against biotic stressors with enhanced biosynthesis of terpenoids, cinnamic acids, and other secondary metabolites. The Sus seedlings showed defense responses to abiotic stimuli with a few biological processes enhanced (such as DNA replication and cell wall organization), while others were suppressed (such as killing of cells of other organism). Furthermore, non-synonymous single nucleotide polymorphisms (ns-SNPs) of the defense- and resistance-related genes were characterized with high genetic variability. Both phylogenetic analysis and principal coordinate analysis (PCoA) revealed distinct evolutionary distances among the samples. The QR and Sus seedlings were well separated and grouped into different phylogenetic clades. This study provides initial insight into molecular defense and genetic components of western hemlock resistance against the Annosus root and butt rot disease. Identification of a large number of genes and their DNA variations with annotated functions in plant resistance and defense promotes the development of genomics-based breeding strategies for improved western hemlock resistance to H. occidentale.

The Role of Hydroxycinnamic Acid Amide Pathway in Plant Immunity

The compounds involved in the hydroxycinnamic acid amide (HCAA) pathway are an important class of metabolites in plants. Extensive studies have reported that a variety of plant hydroxycinnamamides exhibit pivotal roles in plant-pathogen interactions, such as p-coumaroylagmatine and ferulic acid. The aim of this review is to discuss the emerging findings on the functions of hydroxycinnamic acid amides (HCAAs) accumulation associated with plant defenses against plant pathologies, antimicrobial activity of HCAAs, and the mechanism of HCAAs involved in plant immune responses (such as reactive oxygen species (ROS), cell wall response, plant defense hormones, and stomatal immunity). However, these advances have also revealed the complexity of HCAAs participation in plant defense reactions, and many mysteries remain to be revealed. This review provides an overview of the mechanistic and conceptual insights obtained so far and highlights areas for future exploration of phytochemical defense metabolites.

Preinoculation with Endophytic fungus Phomopsis liquidambaris reduced rice bakanae disease caused by Fusarium proliferatum via enhanced plant resistance

AIMS

This study evaluated the control effect of the endophytic fungus Phomopsis liquidambaris B3 against rice bakanae disease (RBD) caused by Fusarium proliferatum and the disease control result of different inoculation times of beneficial micro-organisms.

METHODS AND RESULTS

Rice seedlings preinoculated, coinoculated and noninoculated with B3 were exposed to F. proliferatum stress and grown under controlled conditions. Greenhouse experimental results showed that rice preinoculation with B3 significantly reduced rice bakanae disease by 21.45%, inhibited the colonization of F. proliferatum, increased defence-related enzyme activities, upregulated the expression of defence genes and promoted plant photosynthesis. However, bakanae disease in rice coinoculation with B3 increased by 11.45%, resulted in excessive reactive oxygen species (ROS) bursts and plant cell death.

CONCLUSIONS

Preinoculation with the endophytic fungus P. liquidambaris B3 significantly reduced rice bakanae disease by triggering the SA-dependent defence pathways of plants, and promoted plant growth. However, coinoculatiton with P. liquidambaris B3 activated excessive defence responses, resulting in plants cell death and aggravation of bakanae disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that P. liquidambaris B3 was an effective method for agricultural control against rice bakanae disease caused by F. proliferatum, and provides an experimental basis for the development of sustainable endophytic fungal resources to effectively control plant diseases caused by pathogenic fungi, and suggests that precise application of beneficial micro-organisms may be become a key factor in farmland crop disease management.

Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response (HR). This type of cell death occurs precisely at the site of pathogen recognition, and it is restricted to a few cells. Extensive research has shed light on how plant immune receptors are mechanistically activated. However, two central key questions remain largely unresolved: how does cell death zonation take place, and what are the mechanisms that underpin this phenomenon? Consequently, bona fide transcriptional indicators of HR are lacking, which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation. In this study, to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana-Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity. Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes, expression profiles, and biological processes derived from tissue undergoing HR and that of its surroundings. Furthermore, we generated a pipeline based on concatenated pairwise comparisons between time, zone, and treatment that enabled us to define 13 robust transcriptional HR markers. Among these genes, the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death. This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria, opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level.

The Effects of Rhizosphere Inoculation with Pseudomonas mandelii on Formation of Apoplast Barriers, HvPIP2 Aquaporins and Hydraulic Conductance of Barley

Pseudomonas mandelii strain IB-Ki14 has recently been shown to strengthen the apoplastic barriers of salt-stressed plants, which prevents the entry of toxic sodium. It was of interest to find out whether the same effect manifests itself in the absence of salinity and how this affects the hydraulic conductivity of barley plants. Berberine staining confirmed that the bacterial treatment enhanced the deposition of lignin and suberin and formation of Casparian bands in the roots of barley plants. The calculation of hydraulic conductance by relating transpiration to leaf water potential showed that it did not decrease in bacteria-treated plants. We hypothesized that reduced apoplastic conductivity could be compensated by the higher conductivity of the water pathway across the membranes. This assumption was confirmed by the results of the immunolocalization of HvPIP2;5 aquaporins with specific antibodies, showing their increased abundance around the areas of the endodermis and exodermis of bacteria-treated plants. The immunolocalization with antibodies against auxins and abscisic acid revealed elevated levels of these hormones in the roots of plants treated with bacteria. This root accumulation of hormones is likely to be associated with the ability of Pseudomonas mandelii IB-Ki14 to synthesize these hormones. The involvement of abscisic acid in the control of aquaporin abundance and auxins—in the regulation of and formation of apoplast barriers—is discussed.

Plant-microbe interactions in the apoplast: Communication at the plant cell wall

The apoplast is a continuous plant compartment that connects cells between tissues and organs and is one of the first sites of interaction between plants and microbes. The plant cell wall occupies most of the apoplast and is composed of polysaccharides and associated proteins and ions. This dynamic part of the cell constitutes an essential physical barrier and a source of nutrients for the microbe. At the same time, the plant cell wall serves important functions in the interkingdom detection, recognition, and response to other organisms. Thus, both plant and microbe modify the plant cell wall and its environment in versatile ways to benefit from the interaction. We discuss here crucial processes occurring at the plant cell wall during the contact and communication between microbe and plant. Finally, we argue that these local and dynamic changes need to be considered to fully understand plant-microbe interactions.

Molecular innovations in plant TIR-based immunity signaling

A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.

Unveiling Differences in Root Defense Mechanisms Between Tolerant and Susceptible Olive Cultivars to Verticillium dahliae

Verticillium wilt of olive (VWO), caused by the soil-borne vascular pathogen Verticillium dahliae, is one of the most devastating diseases affecting olive, the woody crop. One of the best VWO management measures is the use of tolerant cultivars. Yet, our knowledge about defense mechanisms that operate at the root level to explain tolerance to this disease is incomplete. Moreover, most of the approaches so far followed focus only on a specific mechanistic level (e.g., genetic, physiological, or biochemical) rather than on a holistic/multilevel perspective. In this study, eighteen root functional traits, the time-course expression of nine defense-related genes, the root lignin content, and the root membrane permeability were evaluated in six olive varieties differing in their level of tolerance/susceptibility to VWO. The aim was to find links between the level of tolerance to VWO and specific root defense mechanisms at the structural, genetic, biochemical, and physiological levels. Tolerant and susceptible cultivars showed substantial differences in the root system architecture and root lignin content. VWO-susceptible cultivars presented roots with higher specific length and area, but lower diameter and larger number of forks and tips compared to tolerant varieties that also showed less branched roots, higher root diameter, and larger basal content of lignin. Interestingly, VWO-tolerant varieties significantly increased their root lignin content and root membrane permeability after inoculation with V. dahliae. These results were seldom (or not at all) observed in the susceptible plants. At the genetic level, genes related to defense mechanisms, such as cell wall lignin biosynthesis (C4H and CO-MT), production of hydrolytic enzymes able to degrade the fungal cell wall (β-1.3-glucanase), and activation of innate immunity (BAK1 and WRKY5) increased their expression in tolerant cultivars from early moments after inoculation, in contrast to the susceptible ones. These results showed that differences in the root system architecture and lignin content may greatly determine the performance of olive against colonization and invasion by V. dahliae. Moreover, the increase in root membrane permeability in the presence of the pathogen was a typical response of tolerant cultivars. Finally, VWO-tolerant cultivars were able to mount a more intense and rapid defense-related genetic response to respond to the attack by V. dahliae.