Lignin biosynthesis

A Fenton Approach to Aromatic Radical Cations and Diarylmethane Synthesis

Manipulating carbon-centered radicals to add to electron-deficient systems is a well-precedented process. By coupling the Fe(II)-mediated Fenton reaction with the Fe(III)-mediated single-electron oxidation of anisolic compounds, we demonstrate how electron-rich carbon-centered radicals can react with electron-rich arenes through a radical-polar cascade pathway. This bioinspired approach produces diarylmethane derivatives from simple unfunctionalized precursors.

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localised multicopper oxidase family enzymes LACCASES (LACs) catalyse the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in the root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem wall thickness. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing and STTM397 chickpea lines showed sensitivity and tolerance, respectively, towards natural drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot (DRR) disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to DRR. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and DRR in an agriculturally important crop chickpea.

Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures

Freshwater fungi play an important role in the decomposition of organic matter of leaf litter in rivers and streams. They also possess the necessary mechanisms to endure lower temperatures caused by habitat and weather variations. This includes the production of cold-active enzymes and antifreeze proteins. To better understand the physiological activities of freshwater fungi in their natural environment, different methods are being applied, and genome sequencing is one in the spotlight. In our study, we sequenced the first genome of the freshwater fungus Filosporella fistucella (45.7 Mb) and compared the genome with the evolutionary close-related species Tricladium varicosporioides (48.2 Mb). The genomes were annotated using the carbohydrate-active enzyme database where we then filtered for leaf-litter degradation-related enzymes (cellulase, hemicellulase, laccase, pectinase, cutinase, amylase, xylanase, and xyloglucanase). Those enzymes were analyzed for antifreeze properties using a machine-learning approach. We discovered that F. fistucella has more enzymes to participate in the breakdown of sugar, leaf, and wood than T. varicosporioides (855 and 719, respectively). Filosporella fistucella shows a larger set of enzymes capable of resisting cold temperatures than T. varicosporioides (75 and 66, respectively). Our findings indicate that in comparison with T. varicosporioides, F. fistucella has a greater capacity for aquatic growth, adaptability to freshwater environments, and resistance to low temperatures.

Potassium Phosphite Activates Components Associated with Constitutive Defense Responses in Coffea arabica Cultivars

Phosphites have been used as inducers of resistance, activating the defense of plants and increasing its ability to respond to the invasion of the pathogen. However, the mode of action of phosphites in defense responses has not yet been fully elucidated. The objective of this study was to evaluate the effect of potassium phosphite (KPhi) in coffee cultivars with different levels of resistance to rust to clarify the mechanism by which KPhi activates the constitutive defense of plants. To this end, we studied the expression of genes and the activity of enzymes involved in the defense pathway of salicylic acid (SA) and reactive oxygen species (ROS), in addition to the levels of total soluble phenolic compounds and soluble lignin. Treatment with KPhi induced constitutive defense responses in cultivars resistant and susceptible to rust. The results suggest that KPhi acts in two parallel defense pathways, SA and ROS, which are essential for the induction of systemic acquired resistance (SAR) when activated simultaneously. The activation of the mechanisms associated with defense routes demonstrates that KPhi is a potential inducer of resistance in coffee plants.

The isolation of lignin with native-like structure

Searching for renewable alternatives for fossil carbon resources to produce chemicals, fuels and materials is essential for the development of a sustainable society. Lignin, a major component of lignocellulosic biomass, is an abundant renewable source of aromatics and is currently underutilized as it is often burned as an undesired side stream in the production of paper and bioethanol. This lignin harbors great potential as source of high value aromatic chemicals and materials. Biorefinery schemes focused on lignin are currently under development with aim of acquiring added value from lignin. However, the performance of these novel lignin-focused biorefineries is closely linked with the quality of extracted lignin in terms of the level of degradation and modification. Thus, the reactivity including the degradation pathways of the native lignin contained in the plant material needs to be understood in detail to potentially achieve higher value from lignin. Undegraded native-like lignin with an as close as possible structure to native lignin contained in the lignocellulosic plant material serves as a promising model lignin to support detailed studies on the structure and reactivity of native lignin, yielding key understanding for the development of lignin-focused biorefineries. The aim of this review is to highlight the different methods to attain "native-like" lignins that can be valuable for such studies. This is done by giving a basic introduction on what is known about the native lignin structure and the techniques and methods used to analyze it followed by an overview of the fractionation and isolation methods to isolate native-like lignin. Finally, a perspective on the isolation and use of native-like lignin is provided, showing the great potential that this type of lignin brings for understanding the effect of different biomass treatments on the native lignin structure.

Metabolic Rewiring in Tea Plants in Response to Gray Blight Disease Unveiled by Multi-Omics Analysis

Gray blight disease, which is caused by Pestalotiopsis-like species, poses significant challenges to global tea production. However, the comprehensive metabolic responses of tea plants during gray blight infection remain understudied. Here, we employed a multi-omics strategy to characterize the temporal transcriptomic and metabolomic changes in tea plants during infection by Pseudopestalotiopsis theae, the causal agent of gray blight. Untargeted metabolomic profiling with ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS) revealed extensive metabolic rewiring over the course of infection, particularly within 24 h post-inoculation. A total of 64 differentially accumulated metabolites were identified, including elevated levels of antimicrobial compounds such as caffeine and (-)-epigallocatechin 3-gallate, as well as oxidative catechin polymers like theaflavins, theasinensins and theacitrins. Conversely, the synthesis of (+)-catechin, (-)-epicatechin, oligomeric proanthocyanidins and flavonol glycosides decreased. Integrated omics analyses uncovered up-regulation of phenylpropanoid, flavonoid, lignin biosynthesis and down-regulation of photosynthesis in response to the pathogen stress. This study provides novel insights into the defense strategies of tea plants against gray blight disease, offering potential targets for disease control and crop improvement.

Spraying chitosan on cassava roots reduces postharvest deterioration by promoting wound healing and inducing disease resistance

Postharvest damage makes cassava roots vulnerable to pathogen infections and decay, which significantly hinders the development of the cassava industry. The objective of this study was to assess the antibacterial properties of chitosan in vitro, as well as its effect on wound healing and resistance in cassava roots. The findings demonstrated that the bacteriostatic effect of chitosan became increasingly prominent as the concentration of chitosan enhanced. Chitosan at a concentration of 0.5 mg/mL was revealed to significantly inhibit the germination of P. palmivora spores and damage to their structure. Moreover, chitosan activated the transcription of crucial genes and enzyme activities associated with the phenylpropane metabolism pathway in cassava roots, thus promoting rapid lignin accumulation and resulting in the early formation of a fracture layer. Chitosan was also found to enhance cassava root resistance by promoting the expression of pathogenesis-related proteins and the accumulation of flavonoids and total phenols. After 48 h of inoculation, cassava roots treated with chitosan exhibited a 51.4 % and 53.4 % decrease in lesion area for SC9 and SC6 varieties, respectively. The findings of this study offer a novel approach for managing postharvest deterioration of cassava roots.

Evaluating potential of leaf reflectance spectra to monitor plant genetic variation

Remote sensing of vegetation by spectroscopy is increasingly used to characterize trait distributions in plant communities. How leaves interact with electromagnetic radiation is determined by their structure and contents of pigments, water, and abundant dry matter constituents like lignins, phenolics, and proteins. High-resolution ("hyperspectral") spectroscopy can characterize trait variation at finer scales, and may help to reveal underlying genetic variation-information important for assessing the potential of populations to adapt to global change. Here, we use a set of 360 inbred genotypes of the wild coyote tobacco Nicotiana attenuata: wild accessions, recombinant inbred lines (RILs), and transgenic lines (TLs) with targeted changes to gene expression, to dissect genetic versus non-genetic influences on variation in leaf spectra across three experiments. We calculated leaf reflectance from hand-held field spectroradiometer measurements covering visible to short-wave infrared wavelengths of electromagnetic radiation (400-2500 nm) using a standard radiation source and backgrounds, resulting in a small and quantifiable measurement uncertainty. Plants were grown in more controlled (glasshouse) or more natural (field) environments, and leaves were measured both on- and off-plant with the measurement set-up thus also in more to less controlled environmental conditions. Entire spectra varied across genotypes and environments. We found that the greatest variance in leaf reflectance was explained by between-experiment and non-genetic between-sample differences, with subtler and more specific variation distinguishing groups of genotypes. The visible spectral region was most variable, distinguishing experimental settings as well as groups of genotypes within experiments, whereas parts of the short-wave infrared may vary more specifically with genotype. Overall, more genetically variable plant populations also showed more varied leaf spectra. We highlight key considerations for the application of field spectroscopy to assess genetic variation in plant populations.

The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis

Abscission is predetermined in specialized cell layers called the abscission zone (AZ) and activated by developmental or environmental signals. In the grass family, most identified AZ genes regulate AZ anatomy, which differs among lineages. A YABBY transcription factor, SHATTERING1 (SH1), is a domestication gene regulating abscission in multiple cereals, including rice and Setaria. In rice, SH1 inhibits lignification specifically in the AZ. However, the AZ of Setaria is nonlignified throughout, raising the question of how SH1 functions in species without lignification. Crispr-Cas9 knockout mutants of SH1 were generated in Setaria viridis and characterized with histology, cell wall and auxin immunofluorescence, transmission electron microscopy, hormonal treatment and RNA-Seq analysis. The sh1 mutant lacks shattering, as expected. No differences in cell anatomy or cell wall components including lignin were observed between sh1 and the wild-type (WT) until abscission occurs. Chloroplasts degenerated in the AZ of WT before abscission, but degeneration was suppressed by auxin treatment. Auxin distribution and expression of auxin-related genes differed between WT and sh1, with the signal of an antibody to auxin detected in the sh1 chloroplast. SH1 in Setaria is required for activation of abscission through auxin signaling, which is not reported in other grass species.

Metabolic Fate of Lignin in Birch Glucuronoxylan Extracts as Dietary Fiber Studied in a Rat Model

SCOPE

While previously considered inert, recent studies suggest lignin metabolism with unknown metabolic fates is occurring in the gastrointestinal tract of several animal models. This study focuses on analyzing the potential metabolites of lignin.

METHODS AND RESULTS

The diets of rats include relatively pure birch glucuronoxylan (pureGX) with residual lignin or lignin-rich GX (GXpoly) in their diet. Nuclear magnetic spectroscopy of the lignin isolated from the GXpoly-fed rats fecal sample shows high alteration in chemical structure, whereas lignin-carbohydrate complexes (LCCs) are enriched in fecal samples from the pureGX group. Moreover, the increased syringyl-to-guaiacyl (S/G) ratio suggests that lignin G-units are predominantly metabolized based on pyrolysis gas chromatography-mass spectrometry (pyr-GC/MS). The presence of small phenolic metabolites identified in urine samples of the GXpoly group, for example, ferulic and sinapic acids, their sulfate and glucuronide derivatives, and 4-sulfobenzylalcohol, suggests that the small fragmented lignin metabolites in the large intestine enter the plasma, and are further processed in the liver. Finally, the relative abundances of polyphenol-degrading Enterorhabdus and Akkermansia in the gut microbiota are associated with lignin metabolism.

CONCLUSION

These findings give further evidence to lignin metabolism in the gut of nonruminants and provide insight to the potential microbes and metabolic routes.

Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain

Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.

Reductive catalytic fractionation as a novel pretreatment/lignin-first approach for lignocellulosic biomass valorization: A review

Presently, the use of lignocellulosic biomass is mainly focused on creating pulp/paper, energy, sugars and bioethanol from the holocellulose component, leaving behind lignin to be discarded or burned as waste despite of its highest aromatic carbon and energy content (22-29 KJ/g). During the pulping process, lignin undergoes significant structural changes to yield technical lignin. For a circular bioeconomy, there is an urgent need to enhance the use of native lignin for generating more valuable products. Over the last few years, a new method called 'lignin-first', or 'reductive catalytic fractionation' (RCF), has been devised to achieve selective phenolic monomers under mild reaction conditions. This involves deconstructing lignin before capitalizing on carbohydrates. The objective of this study is to record the recent developments of the 'lignin-first' process. This review also underlines the contribution of RCF biorefinery towards achieving sustainable development goals (SDGs) and concludes with an overview of challenges and upcoming opportunities.

Biochemical and in silico molecular study of caffeic acid-O-methyltransferase enzyme associated with lignin deposition in tall fescue

Caffeic acid-O-methyltransferase (COMT), an important enzyme governing the process of lignification in plants, functions at the level of caffeic acid methylation along with 3-O-methylation of monolignol precursors. The present investigation was carried out to decipher the role of COMT in tall fescue lignification and to clone and characterize the COMT gene. The study on COMT activity variation at different growth stages of tall fescue exhibited a significant increase in activity over all the growth stages of tall fescue. A significant relative increase of 47.8% was observed from the first vegetative to reproductive stage. COMT activity exhibited a strong positive correlation with lignin content suggesting it to be an important enzyme of tall fescue lignification. Amplification and sequencing of tall fescue COMT gene resulted in an amplicon of size 1662 (Accession No.-MW442832) and an ORF of 346 amino acids. The deduced protein was hydrophobic, thermally stable and acidic with molecular formula C1679H2623N445O482S20, molecular mass 37.4 kDa and theoretical pI of 6.12. The protein possesses a conserved dimerization domain with a highly conserved SAM binding site. The COMT protein was found to be a homo-dimer with 1 catalytic SAH/SAM ligand per monomer interacting with 14 amino acid residues within 4 Å region.

Resolving the influence of lignin on soil organic matter decomposition with mechanistic models and continental-scale data

Confidence in model estimates of soil CO2 flux depends on assumptions regarding fundamental mechanisms that control the decomposition of litter and soil organic carbon (SOC). Multiple hypotheses have been proposed to explain the role of lignin, an abundant and complex biopolymer that may limit decomposition. We tested competing mechanisms using data-model fusion with modified versions of the CN-SIM model and a 571-day laboratory incubation dataset where decomposition of litter, lignin, and SOC was measured across 80 soil samples from the National Ecological Observatory Network. We found that lignin decomposition consistently decreased over time in 65 samples, whereas in the other 15 samples, lignin decomposition subsequently increased. These "lagged-peak" samples can be predicted by low soil pH, high extractable Mn, and fungal community composition as measured by ITS PC2 (the second principal component of an ordination of fungal ITS amplicon sequences). The highest-performing model incorporated soil biogeochemical factors and daily dynamics of substrate availability (labile bulk litter:lignin) that jointly represented two hypotheses (C substrate limitation and co-metabolism) previously thought to influence lignin decomposition. In contrast, models representing either hypothesis alone were biased and underestimated cumulative decomposition. Our findings reconcile competing hypotheses of lignin decomposition and suggest the need to precisely represent the role of lignin and consider soil metal and fungal characteristics to accurately estimate decomposition in Earth-system models.

Heterotic gains, transgressive segregation and fitness cost of sweetpotato weevil resistance expression in a partial diallel cross of sweetpotato

Heterosis-exploiting breeding schemes are currently under consideration as a means of accelerating genetic gains in sweetpotato (Ipomoea batatas) breeding. This study was aimed at establishing heterotic gains, fitness costs and transgressive segregation associated with sweetpotato weevil (SPW) resistance in a partial diallel cross of sweetpotato. A total of 1896 clones were tested at two sites, for two seasons each in Uganda. Data on weevil severity (WED), weevil incidence (WI), storage root yield (SRY) and dry matter content (DM) were obtained. Best linear unbiased predictors (BLUPs) for each clone across environments were used to estimate heterotic gains and for regression analyses to establish relationships between key traits. In general, low mid-parent heterotic gains were detected with the highest favorable levels recorded for SRY (14.7%) and WED (- 7.9%). About 25% of the crosses exhibited desirable and significant mid-parent heterosis for weevil resistance. Over 16% of the clones displayed superior transgressive segregation, with the highest percentages recorded for SRY (21%) and WED (18%). A yield penalty of 10% was observed to be associated with SPW resistance whereas no decline in DM was detected in relation to the same. Chances of improving sweetpotato through exploiting heterosis in controlled crosses using parents of mostly similar background are somewhat minimal, as revealed by the low heterotic gains. The yield penalty detected due to SPW resistance suggests that a trade-off may be necessary between maximizing yields and developing weevil-resistant cultivars if the current needs for this crop are to be met in weevil-prone areas.

Metabolomic and transcriptomic analyses of rice plant interaction with invasive weed Leptochloa chinensis

Introduction

Leptochloa chinensis is an annual weed in paddy fields, which can engage in competition with rice, leading to a severe yield reduction. However, theunderlying mechanism governing this interaction remain unknown.

Methods

In this study, we investigated the mutual inhibition between rice and the weed undermono-culture and co-culture conditions. We found that the root exudates of both species played essential roles in mediating the mutual inhibition. Further metabolomic analysis identified a significant number of differential metabolites. These metabolites were predominantly enriched in the phenylpropanoid and flavonoid biosynthesis pathways in weed and rice. Transcriptomic analysis revealed that the differentially expressed genes responding to the interaction were also enriched in these pathways.

Results

Phenylpropanoid and flavonoid biosynthesis pathways are associated with allelopathy, indicating their pivotal role in the response of rice-weed mutual inhibition.

Discussion

Our findings shed light on the conserved molecular responses of rice and L. chinensis during theirinteraction, provide evidence to dissect the mechanisms underlying the allelopathic interaction and offer potential strategies for weed management in rice paddies.

Jasmonate signaling drives defense responses against Alternaria alternata in chrysanthemum

BACKGROUND

Black spot disease caused by the necrotrophic fungus Alternaria spp. is one of the most devastating diseases affecting Chrysanthemum morifolium. There is currently no effective way to prevent chrysanthemum black spot.

RESULTS

We revealed that pre-treatment of chrysanthemum leaves with the methy jasmonate (MeJA) significantly reduces their susceptibility to Alternaria alternata. To understand how MeJA treatment induces resistance, we monitored the dynamics of metabolites and the transcriptome in leaves after MeJA treatment following A. alternata infection. JA signaling affected the resistance of plants to pathogens through cell wall modification, Ca2+ regulation, reactive oxygen species (ROS) regulation, mitogen-activated protein kinase cascade and hormonal signaling processes, and the accumulation of anti-fungal and anti-oxidant metabolites. Furthermore, the expression of genes associated with these functions was verified by reverse transcription quantitative PCR and transgenic assays.

CONCLUSION

Our findings indicate that MeJA pre-treatment could be a potential orchestrator of a broad-spectrum defense response that may help establish an ecologically friendly pest control strategy and offer a promising way of priming plants to induce defense responses against A. alternata.

Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities

The diversification of effector function, driven by a co-evolutionary arms race, enables pathogens to establish compatible interactions with hosts. Structurally conserved plant pathogenesis-related PR-1 and PR-1-like (PR-1L) proteins are involved in plant defense and fungal virulence, respectively. It is unclear how fungal PR-1L counters plant defense. Here, we show that Ustilago maydis UmPR-1La and yeast ScPRY1, with conserved phenolic resistance functions, are Ser/Thr-rich region mediated cell-surface localization proteins. However, UmPR-1La has gained specialized activity in sensing phenolics and eliciting hyphal-like formation to guide fungal growth in plants. Additionally, U. maydis hijacks maize cathepsin B-like 3 (CatB3) to release functional CAPE-like peptides by cleaving UmPR-1La's conserved CNYD motif, subverting plant CAPE-primed immunity and promoting fungal virulence. Surprisingly, CatB3 avoids cleavage of plant PR-1s, despite the presence of the same conserved CNYD motif. Our work highlights that UmPR-1La has acquired additional dual roles to suppress plant defense and sustain the infection process of fungal pathogens.

Integrative analysis of metabolome, proteome, and transcriptome for identifying genes influencing total lignin content in Populus trichocarpa

Lignin, a component of plant cell walls, possesses significant research potential as a renewable energy source to replace carbon-based products and as a notable pollutant in papermaking processes. The monolignol biosynthetic pathway has been elucidated and it is known that not all monolignol genes influence the total lignin content. However, it remains unclear which monolignol genes are more closely related to the total lignin content and which potential genes influence the total lignin content. In this study, we present a combination of t-test, differential gene expression analysis, correlation analysis, and weighted gene co-expression network analysis to identify genes that regulate the total lignin content by utilizing multi-omics data from transgenic knockdowns of the monolignol genes that includes data related to the transcriptome, proteome, and total lignin content. Firstly, it was discovered that enzymes from the PtrPAL, Ptr4CL, PtrC3H, and PtrC4H gene families are more strongly correlated with the total lignin content. Additionally, the co-downregulation of three genes, PtrC3H3, PtrC4H1, and PtrC4H2, had the greatest impact on the total lignin content. Secondly, GO and KEGG analysis of lignin-related modules revealed that the total lignin content is not only influenced by monolignol genes, but also closely related to genes involved in the "glutathione metabolic process", "cellular modified amino acid metabolic process" and "carbohydrate catabolic process" pathways. Finally, the cinnamyl alcohol dehydrogenase genes CAD1, CADL3, and CADL8 emerged as potential contributors to total lignin content. The genes HYR1 (UDP-glycosyltransferase superfamily protein) and UGT71B1 (UDP-glucosyltransferase), exhibiting a close relationship with coumarin, have the potential to influence total lignin content by regulating coumarin metabolism. Additionally, the monolignol genes PtrC3H3, PtrC4H1, and PtrC4H2, which belong to the cytochrome P450 genes, may have a significant impact on the total lignin content. Overall, this study establishes connections between gene expression levels and total lignin content, effectively identifying genes that have a significant impact on total lignin content and offering novel perspectives for future lignin research endeavours.

Fluorescent optotracers for bacterial and biofilm detection and diagnostics

Effective treatment of bacterial infections requires methods that accurately and quickly identify which antibiotic should be prescribed. This review describes recent research on the development of optotracing methodologies for bacterial and biofilm detection and diagnostics. Optotracers are small, chemically well-defined, anionic fluorescent tracer molecules that detect peptide- and carbohydrate-based biopolymers. This class of organic molecules (luminescent conjugated oligothiophenes) show unique electronic, electrochemical and optical properties originating from the conjugated structure of the compounds. The photophysical properties are further improved as donor-acceptor-donor (D-A-D)-type motifs are incorporated in the conjugated backbone. Optotracers bind their biopolymeric target molecules via electrostatic interactions. Binding alters the optical properties of these tracer molecules, shown as altered absorption and emission spectra, as well as ON-like switch of fluorescence. As the optotracer provides a defined spectral signature for each binding partner, a fingerprint is generated that can be used for identification of the target biopolymer. Alongside their use for in situ experimentation, optotracers have demonstrated excellent use in studies of a number of clinically relevant microbial pathogens. These methods will find widespread use across a variety of communities engaged in reducing the effect of antibiotic resistance. This includes basic researchers studying molecular resistance mechanisms, academia and pharma developing new antimicrobials targeting biofilm infections and tests to diagnose biofilm infections, as well as those developing antibiotic susceptibility tests for biofilm infections (biofilm-AST). By iterating between the microbial world and that of plants, development of the optotracing technology has become a prime example of successful cross-feeding across the boundaries of disciplines. As optotracers offers a capacity to redefine the way we work with polysaccharides in the microbial world as well as with plant biomass, the technology is providing novel outputs desperately needed for global impact of the threat of antimicrobial resistance as well as our strive for a circular bioeconomy.

Transcriptome features of stone cell development in weevil-resistant and susceptible Sitka spruce

Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect-resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell-type-specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.

Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses

The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.

Microbial carbon use efficiency in different ecosystems: A meta-analysis based on a biogeochemical equilibrium model

Soil microbial carbon use efficiency (CUE) is a crucial parameter that can be used to evaluate the partitioning of soil carbon (C) between microbial growth and respiration. However, general patterns of microbial CUE among terrestrial ecosystems (e.g., farmland, grassland, and forest) remain controversial. To address this knowledge gap, data from 41 study sites (n = 197 soil samples) including 58 farmlands, 95 forests, and 44 grasslands were collected and analyzed to estimate microbial CUEs using a biogeochemical equilibrium model. We also evaluated the metabolic limitations of microbial growth using an enzyme vector model and the drivers of CUE across different ecosystems. The CUEs obtained from soils of farmland, forest, and grassland ecosystems were significantly different with means of 0.39, 0.33, and 0.42, respectively, illustrating that grassland soils exhibited higher microbial C sequestration potentials (p < .05). Microbial metabolic limitations were also distinct in these ecosystems, and carbon limitation was dominant exhibiting strong negative effects on CUE. Exoenzyme stoichiometry played a greater role in impacting CUE values than soil elemental stoichiometry within each ecosystem. Specifically, soil exoenzymatic ratios of C:phosphorus (P) acquisition activities (EEAC:P ) and the exoenzymatic ratio of C:nitrogen (N) acquisition activities (EEAC:N ) imparted strong negative effects on soil microbial CUE in grassland and forest ecosystems, respectively. But in farmland soils, EEAC:P exhibited greater positive effects, showing that resource constraints could regulate microbial resource allocation with discriminating patterns across terrestrial ecosystems. Furthermore, mean annual temperature (MAT) rather than mean annual precipitation (MAP) was a critical climate factor affecting CUE, and soil pH as a major factor remained positive to drive the changes in microbial CUE within ecosystems. This research illustrates a conceptual framework of microbial CUEs in terrestrial ecosystems and provides the theoretical evidence to improve soil microbial C sequestration capacity in response to global change.

Antioxidant Activity of Biogenic Cinnamic Acid Derivatives in Polypropylene

Antioxidants (AOs) from natural resources are an attractive research area, as petroleum-based products can be replaced in polymer stabilization. Therefore, novel esters based on the p-hydroxycinnamic acids p-coumaric acid, ferulic acid and sinapic acid were synthesized and their structure properties relationships were investigated. The structures of the novel bio-based antioxidants were verified using NMR and Fourier-transform infrared (FTIR) spectrometry. The high thermal stability above 280 °C and, therefore, their suitability as potential plastic stabilizers were shown using thermal gravimetric analysis (TGA). The radical scavenging activity of the synthesized esters was evaluated by using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Stabilization performance was evaluated in polypropylene (PP) using extended extrusion experiments, oxidation induction time (OIT) measurements and accelerated heat aging. In particular, the sinapic acid derivative provides a processing stability of PP being superior to the commercial state-of-the-art stabilizer octadecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate.

Water-Soluble Alkali Lignin as a Natural Radical Scavenger and Anticancer Alternative

Several phytochemicals, which display antioxidant activity and inhibit cancer cell phenotypes, could be used for cancer treatment and prevention. Lignin, as a part of plant biomass, is the second most abundant natural biopolymer worldwide, and represents approximately 30% of the total organic carbon content of the biosphere. Historically, lignin-based products have been viewed as waste materials of limited industrial usefulness, but modern technologies highlight the applicability of lignin in a variety of industrial branches, including biomedicine. The aims of our preliminary study were to compare the antioxidant properties of water-soluble alkali lignin solutions, before and after UV-B irradiation, as well as to clarify their effect on colon cancer cell viability (Colon 26), applied at low (tolerable) concentrations. The results showed a high antioxidant capacity of lignin solutions, compared to a water-soluble control antioxidant standard (Trolox) and remarkable radical scavenging activity was observed after their UV-B irradiation. Diminishment of cell viability as well as inhibition of the proliferative activity of the colon cancer cell line with an increase in alkali lignin concentrations were observed. Our results confirmed that, due to its biodegradable and biocompatible nature, lignin could be a potential agent for cancer therapy, especially in nanomedicine as a drug delivery system.

Caffeoyl-coenzyme A O-methyltransferase mediates regulation of carbon flux fluctuations during phenylpropenes and lignin biosynthesis in the vegetative organ roots of Asarum sieboldii Miq

Asarum sieboldii Miq. possesses remarkable medicinal value due to its essential oil enriched with phenylpropenes (e.g., methyleugenol and safrole). Although the biosynthesis of phenylpropenes shares a common pathway with lignin, the regulation mechanisms in carbon flux allocation between them are unclear. This study is the first to genetically verify the carbon flux regulation mechanism in A. sieboldii roots. We regulated the expression of Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT), an essential enzyme in the common pathway, to investigate carbon flux allocation in vegetative organs. Here, the lignin and phenylpropene content fluctuation was analyzed by wet chemistry and GC-MS methods. A bona fide CCoAOMT gene from A. sieboldii was firstly cloned and verified. Preliminary heterologous expression validation in transgenic Arabidopsis thaliana showed that RNAi-induced CCoAOMT down-regulation significantly decreased lignin content by 24% and increased the S/G ratio by 30%; however, AsCCoAOMT over-expression in A. thaliana resulted in a 40% increase in lignin content and a 20% decrease in the S/G ratio when compared to the wild type. Similar trends were noted in homologous transformation in A. sieboldii, although the variations were not conspicuous. Nevertheless, the transgenic A. sieboldii plants displayed substantial differences in the level of phenylpropene compounds methyleugenol and safrole leading to a 168% increase in the methyleugenol/safrole ratio in the over-expression line and a 73% reduction in RNAi-suppression line. These findings suggest that the biosynthesis of phenylpropene constituents methyleugenol and safrole seems to be prioritized over lignin. Furthermore, this study indicated that suppression of AsCCoAOMT resulted in marked root susceptibility to pathogenic fungal disease, implying a significant additional role of CCoAOMT in protecting plant vegetative parts from diseases. Overall, the present study provides important references and suggests that future research should be aimed at elucidating the detailed mechanisms of the carbon flux allocation between phenylpropenes and lignin biosynthesis, as well as the disease resistance competency.

Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger

Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl-CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate.

Meyerozyma guilliermondii promoted the deposition of GSH type lignin by activating the biosynthesis and polymerization of monolignols at the wounds of potato tubers

Lignin is a crucial component in the wound tissue of tubers. The biocontrol yeast Meyerozyma guilliermondii increased the activities of phenylalanine ammonia lyase, cinnamate-4-hydroxylase, 4-coenzyme coenzyme A ligase, and cinnamyl alcohol dehydrogenase, and elevated the levels of coniferyl, sinapyl, and p-coumaryl alcohol. The yeast also enhanced the activities of peroxidase and laccase, as well as the content of hydrogen peroxide. The lignin promoted by the yeast was identified as guaiacyl-syringyl-p-hydroxyphenyl type using Fourier transform infrared spectroscopy and two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance. Furthermore, a larger signal area for G₂, G₅, G'₆, S_{2, 6}, and S'_{2, 6} units was observed in the treated tubers, and the G'₂ and G₆ units were only detected in the treated tuber. Taken together, M. guilliermondii could promote deposition of guaiacyl-syringyl-p-hydroxyphenyl type lignin by activating the biosynthesis and polymerization of monolignols at the wounds of potato tubers.

Kraft Lignin: A Valuable, Sustainable Resource, Opportunities and Challenges

Kraft lignin, a by-product from the production of pulp, is currently incinerated in the recovery boiler during the chemical recovery cycle, generating valuable bioenergy and recycling inorganic chemicals to the pulping process operation. Removing lignin from the black liquor or its gasification lowers the recovery boiler load enabling increased pulp production. During the past ten years, lignin separation technologies have emerged and the interest of the research community to valorize this underutilized resource has been invigorated. The aim of this Review is to give (1) a dedicated overview of the kraft process with a focus on the lignin, (2) an overview of applications that are being developed, and (3) a techno-economic and life cycle asseeements of value chains from black liquor to different products. Overall, it is anticipated that this effort will inspire further work for developing and using kraft lignin as a commodity raw material for new applications undeniably promoting pivotal global sustainability concerns.

Risk Assessment of Chlorogenic and Isochlorogenic Acids in Coffee By-Products

Chlorogenic and isochlorogenic acids are naturally occurring antioxidant dietary polyphenolic compounds found in high concentrations in plants, fruits, vegetables, coffee, and coffee by-products. The objective of this review was to assess the potential health risks associated with the oral consumption of coffee by-products containing chlorogenic and isochlorogenic acids, considering both acute and chronic exposure. An electronic literature search was conducted, revealing that 5-caffeoylquinic acid (5-CQA) and 3,5-dicaffeoylquinic acid (3,5-DCQA) are the major chlorogenic acids found in coffee by-products. Toxicological, pharmacokinetic, and clinical data from animal and human studies were available for the assessment, which indicated no significant evidence of toxic or adverse effects following acute oral exposure. The current state of knowledge suggests that long-term exposure to chlorogenic and isochlorogenic acids by daily consumption does not appear to pose a risk to human health when observed at doses within the normal range of dietary exposure. As a result, the intake of CQAs from coffee by-products can be considered reasonably safe.

Bioderived Laser-Induced Graphene for Sensors and Supercapacitors

The maskless and chemical-free conversion and patterning of synthetic polymer precursors into laser-induced graphene (LIG) via laser-induced pyrolysis is a relatively new but growing field. Bioderived precursors from lignocellulosic materials can also be converted to LIG, opening a path to sustainable and environmentally friendly applications. This review is designed as a starting point for researchers who are not familiar with LIG and/or who wish to switch to sustainable bioderived precursors for their applications. Bioderived precursors are described, and their performances (mainly crystallinity and sheet resistance of the obtained LIG) are compared. The three main fields of application are reviewed: supercapacitors and electrochemical and physical sensors. The key advantages and disadvantages of each precursor for each application are discussed and compared to those of a benchmark of polymer-derived LIG. LIG from bioderived precursors can match, or even outperform, its synthetic analogue and represents a viable and sometimes better alternative, also considering its low cost and biodegradability.

Effect of Molecular Organization on the Properties of Fractionated Lignin-Based Thiol-Ene Thermoset Materials

In this study, the combination of sequential solvent fractionation of technical Kraft lignin was followed by allylation of most OH functionalities to give highly functional thermoset resins. All lignin fractions were highly functionalized on the phenolic (≥95%) and carboxylic acid OH (≥85%) and to a significant extent on the aliphatic OH moieties (between 43 and 75%). The resins were subsequently cross-linked using thiol-ene chemistry. The high amount of allyl functionalities resulted in a high cross-link density. Dynamic mechanical analysis measurements showed that the thioether content, directly related to the allyl content, strongly affects the performance of these thermosets with a glass transition temperature (T_g) between 81 and 95 °C and with a storage modulus between 1.9 and 3.8 GPa for all thermosets. The lignin fractions and lignin-based thermosets' morphology, at the nanoscale, was studied by wide-angle X-ray scattering measurements. Two π-π stacking interactions were observed: sandwich (≈4.1-4.7 Å) and T-shaped (≈5.5-7.2 Å). The introduction of allyl functionalities weakens the T-shaped π-π stacking interactions. A new signal corresponding to a distance of ≈3.5 Å was observed in lignin-based thermosets, which was attributed to a thioether organized structure. At the same time, a lignin superstructure was observed with a distance/size corresponding to 7.9-17.5 Å in all samples.

Multiplex CRISPR editing of wood for sustainable fiber production

The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.

Metabolic profiling reveals key metabolites regulating adventitious root formation in ancient Platycladus orientalis cuttings

Platycladus orientalis, a common horticultural tree species, has an extremely long life span and forms a graceful canopy. Its branches, leaves, and cones have been used in traditional Chinese medicine. However, difficulty in rooting is the main limiting factor for the conservation of germplasm resources. This study shows that the rooting rates and root numbers of cuttings were significantly reduced in ancient P. orientalis donors compared to 5-year-old P. orientalis donors. The contents of differentially accumulated metabolites (DAMs) in phenylpropanoid (caffeic acid and coniferyl alcohol) and flavonoid biosynthesis (cinnamoyl-CoA and isoliquiritigenin) pathways increased significantly in cuttings propagated from ancient P. orientalis donors compared to 5-year-old P. orientalis donors during adventitious root (AR) formation. These DAMs may prevent the ancient P. orientalis cuttings from rooting, and gradual lignification of callus was one of the main reasons for the failed rooting of ancient P. orientalis cuttings. The rooting rates of ancient P. orientalis cuttings were improved by wounding the callus to identify wounding-induced rooting-promoting metabolites. After wounding, the contents of DAMs in zeatin (5'-methylthioadenosine, cis-zeatin-O-glucoside, and adenine) and aminoacyl-tRNA biosynthesis (l-glutamine, l-histidine, l-isoleucine, l-leucine, and l-arginine) pathways increased, which might promote cell division and provided energy for the rooting process. The findings of our study suggest that breaking down the lignification of callus via wounding can eventually improve the rooting rates of ancient P. orientalis cuttings, which provides a new solution for cuttings of other difficult-to-root horticultural and woody plants.

Lignin Hydrogenolysis: Phenolic Monomers from Lignin and Associated Phenolates across Plant Clades

The chemical complexity of lignin remains a major challenge for lignin valorization into commodity and fine chemicals. A knowledge of the lignin features that favor its valorization and which plants produce such lignins can be used in plant selection or to engineer them to produce lignins that are more ideally suited for conversion. Sixteen biomass samples were compositionally surveyed by NMR and analytical degradative methods, and the yields of phenolic monomers following hydrogenolytic depolymerization were assessed to elucidate the key determinants controlling the depolymerization. Hardwoods, including those incorporating monolignol p-hydroxybenzoates into their syringyl/guaiacyl copolymeric lignins, produced high monomer yields by hydrogenolysis, whereas grasses incorporating monolignol p-coumarates and ferulates gave lower yields, on a lignin basis. Softwoods, with their more condensed guaiacyl lignins, gave the lowest yields. Lignins with a high syringyl unit content released elevated monomer levels, with a high-syringyl polar transgenic being particularly striking. Herein, we distinguish phenolic monomers resulting from the core lignin vs those from pendent phenolate esters associated with the biomass cell wall, acylating either polysaccharides or lignins. The basis for these observations is rationalized as a means to select or engineer biomass for optimal conversion to worthy phenolic monomers.

Optimization of Approaches to Analysis of Lignin by Thermal Decomposition

The ratio of monomeric units is one of the main characteristics of lignin, which affects the possibilities and strategies for further processing. Pyrolytic and thermal desorption decomposition of lignins followed by mass detection of macromolecule fragments are the most common methods for determining the amount of lignin structural units. Two methods of thermal decomposition of lignin were studied: thermal desorption-GC/MS (TD-GC/MS) and pyrolysis-GC/MS (Py-GC/MS). It was noted that, when using different thermal decomposition modes, the composition of the products changes, which affects the accuracy of determining the amount of lignin structural fragments. This article investigated the influence of the sample weight, the thermal decomposition temperature, and the duration of the process in various modes on the quantitation of the lignin structural units. The optimal process conditions were established. It was shown that the DS-Py-GC/MS with cryofocusing, a sample weight of 0.2-0.4 mg, and heating from 50 to 400 °C at a rate of 120 °C/min are preferable. The HSQC NMR was used as a comparison method to obtain the content of the S/G/H units. The results showed the applicability of the proposed approaches to hardwood lignins close to native.

How to Design Catechol-Containing Hydrogels for Cell Encapsulation Despite Catechol Toxicity

Catechol (cat) is a highly adhesive diphenol that can be chemically grafted to polymers such as chitosan (CH) to make them adhesive as well. However, catechol-containing materials experimentally show a large variability of toxicity, especially in vitro. While it is unclear how this toxicity emerges, most concerns are directed toward the oxidation of catechol into quinone that releases reactive oxygen species (ROS) which can, in turn, cause cell apoptosis through oxidative stress. To better understand the mechanisms at play, we examined the leaching profiles, hydrogen peroxide (H₂O₂) production, and in vitro cytotoxicity of several cat-chitosan (cat-CH) hydrogels that were prepared with different oxidation levels and cross-linking methods. To create cat-CH with different propensities toward oxidation, we grafted either hydrocaffeic acid (HCA, more prone to oxidation) or dihydrobenzoic acid (DHBA, less prone to oxidation) to the backbone of CH. Hydrogels were cross-linked either covalently, using sodium periodate (NaIO₄) to trigger oxidative cross-linking, or physically, using sodium bicarbonate (SHC). While using NaIO₄ as a cross-linker increased the oxidation levels of the hydrogels, it also significantly reduced in vitro cytotoxicity, H₂O₂ production, and catechol and quinone leaching in the media. For all gels tested, cytotoxicity could be directly related to the release of quinones rather than H₂O₂ production or catechol release, showing that oxidative stress may not be the main reason for catechol cytotoxicity, as other pathways of quinone toxicity come into play. Results also suggest that the indirect cytotoxicity of cat-CH hydrogels fabricated through carbodiimide chemistry can be reduced if (i) catechol groups are chemically bound to the polymer backbone to prevent leaching or (ii) the chosen cat-bearing molecule has a high resistance to oxidation. Coupled with the use of other cross-linking chemistries or more efficient purification methods, these strategies can be adopted to synthesize various types of cytocompatible cat-containing scaffolds.

Integrated transcriptomics and metabolomics analysis provide insight into the resistance response of rice against brown planthopper

Introduction

The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most economically significant pests of rice. The Bph30 gene has been successfully cloned and conferred rice with broad-spectrum resistance to BPH. However, the molecular mechanisms by which Bph30 enhances resistance to BPH remain poorly understood.

Methods

Here, we conducted a transcriptomic and metabolomic analysis of Bph30-transgenic (BPH30T) and BPH-susceptible Nipponbare plants to elucidate the response of Bph30 to BPH infestation.

Results

Transcriptomic analyses revealed that the pathway of plant hormone signal transduction enriched exclusively in Nipponbare, and the greatest number of differentially expressed genes (DEGs) were involved in indole 3-acetic acid (IAA) signal transduction. Analysis of differentially accumulated metabolites (DAMs) revealed that DAMs involved in the amino acids and derivatives category were down-regulated in BPH30T plants following BPH feeding, and the great majority of DAMs in flavonoids category displayed the trend of increasing in BPH30T plants; the opposite pattern was observed in Nipponbare plants. Combined transcriptomics and metabolomics analysis revealed that the pathways of amino acids biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis and flavonoid biosynthesis were enriched. The content of IAA significantly decreased in BPH30T plants following BPH feeding, and the content of IAA remained unchanged in Nipponbare. The exogenous application of IAA weakened the BPH resistance conferred by Bph30.

Discussion

Our results indicated that Bph30 might coordinate the movement of primary and secondary metabolites and hormones in plants via the shikimate pathway to enhance the resistance of rice to BPH. Our results have important reference significance for the resistance mechanisms analysis and the efficient utilization of major BPH-resistance genes.

Lignin Extracted from Various Parts of Castor (Ricinus communis L.) Plant: Structural Characterization and Catalytic Depolymerization

Castor is an important non-edible oilseed crop used in the production of high-quality bio-oil. In this process, the leftover tissues rich in cellulose, hemicellulose and lignin are regarded as by-products and remain underutilized. Lignin is a crucial recalcitrance component, and its composition and structure strongly limit the high-value utilization of raw materials, but there is a lack of detailed studies relating to castor lignin chemistry. In this study, lignins were isolated from various parts of the castor plant, namely, stalk, root, leaf, petiole, seed endocarp and epicarp, using the dilute HCl/dioxane method, and the structural features of the as-obtained six lignins were investigated. The analyses indicated that endocarp lignin contained catechyl (C), guaiacyl (G) and syringyl (S) units, with a predominance of C unit [C/(G+S) = 6.9:1], in which the coexisted C-lignin and G/S-lignin could be disassembled completely. The isolated dioxane lignin (DL) from endocarp had a high abundance of benzodioxane linkages (85%) and a low level of β-β linkages (15%). The other lignins were enriched in G and S units with moderate amounts of β-O-4 and β-β linkages, being significantly different from endocarp lignin. Moreover, only p-coumarate (pCA) incorporated into the epicarp lignin was observed, with higher relative content, being rarely reported in previous studies. The catalytic depolymerization of isolated DL generated 1.4-35.6 wt% of aromatic monomers, among which DL from endocarp and epicarp have high yields and excellent selectivity. This work highlights the differences in lignins from various parts of the castor plant, providing a solid theory for the high-value utilization of the whole castor plant.

Relationship between the Change in E/T Ratio and the Cooking Performance of Eucalyptus and Acacia Woods during Kraft Pulping Process

Lignin structure is an important factor affecting the cooking part of the pulping process. In this study, the effect of lignin side chain spatial configuration on cooking performance was analyzed, and the structural characteristics of eucalyptus and acacia during cooking were compared and studied by combining ozonation, GC-MS, NBO, and 2D NMR (¹H-¹³C HSQC). In addition, the changes in the lignin content of four different raw materials during the cooking process were studied via ball milling and UV spectrum analysis. The results showed that the content of lignin in the raw material decreased continuously during the cooking process. Only in the late cooking stage, when the lignin removal reached its limit, did the lignin content tend to be stable due to the polycondensation reaction of lignin. At the same time, the E/T ratio and S/G ratio of the reaction residual lignin also followed a similar rule. At the beginning of cooking, the values of E/T and S/G decreased rapidly and then gradually rose when they reached a low point. The different initial E/T and S/G values of different raw materials lead to the disunity of cooking efficiency and the different transformation rules of different raw materials in the cooking process. Therefore, the pulping efficiency of different raw materials can be improved using different technological means.

Adhesive and Flame-Retardant Properties of Starch/Ca2+ Gels with Different Amylose Contents

Starch, being renewable and biodegradable, is a viable resource for developing sustainable and environmentally friendly materials. The potential of starch/Ca2+ gels based on waxy corn starch (WCS), normal corn starch (NCS), and two high-amylose corn starches, G50 (55% amylose content) and G70 (68% amylose content) as flame-retardant adhesives has been explored. Being stored at 57% relative humidity (RH) for up to 30 days, the G50/Ca2+ and G70/Ca2+ gels were stable without water absorption or retrogradation. The starch gels with increasing amylose content displayed increased cohesion, as reflected by significantly higher tensile strength and fracture energy. All the four starch-based gels showed good adhesive properties on corrugated paper. For wooden boards, because of the slow diffusion of the gels, the adhesive abilities are weak initially but improve with storage extension. After storage, the adhesive abilities of the starch-based gels are essentially unchanged except for G70/Ca2+, which peels from a wood surface. Moreover, all the starch/Ca2+ gels exhibited excellent flame retardancy with limiting oxygen index (LOI) values all around 60. A facile method for the preparation of starch-based flame-retardant adhesives simply by gelating starch with a CaCl2 solution, which can be used in paper or wood products, has been demonstrated.

Microscopical Analysis of Autofluorescence as a Complementary and Useful Method to Assess Differences in Anatomy and Structural Distribution Underlying Evolutive Variation in Loss of Seed Dispersal in Common Bean

The common bean has received attention as a model plant for legume studies, but little information is available about the morphology of its pods and the relation of this morphology to the loss of seed dispersal and/or the pod string, which are key agronomic traits of legume domestication. Dehiscence is related to the pod morphology and anatomy of pod tissues because of the weakening of the dorsal and ventral dehiscence zones and the tensions of the pod walls. These tensions are produced by the differential mechanical properties of lignified and non-lignified tissues and changes in turgor associated with fruit maturation. In this research, we histologically studied the dehiscence zone of the ventral and dorsal sutures of the pod in two contrasting genotypes for the dehiscence and string, by comparing different histochemical methods with autofluorescence. We found that the secondary cell wall modifications of the ventral suture of the pod were clearly different between the dehiscence-susceptible and stringy PHA1037 and the dehiscence-resistant and stringless PHA0595 genotypes. The susceptible genotype had cells of bundle caps arranged in a more easily breakable bowtie knot shape. The resistant genotype had a larger vascular bundle area and larger fibre cap cells (FCCs), and due to their thickness, the external valve margin cells were significantly stronger than those from PHA1037. Our findings suggest that the FCC area, and the cell arrangement in the bundle cap, might be partial structures involved in the pod dehiscence of the common bean. The autofluorescence pattern at the ventral suture allowed us to quickly identify the dehiscent phenotype and gain a better understanding of cell wall tissue modifications that took place along the bean's evolution, which had an impact on crop improvement. We report a simple autofluorescence protocol to reliably identify secondary cell wall organization and its relationship to the dehiscence and string in the common bean.

The impact of xylan on the biosynthesis and structure of extracellular lignin produced by a Norway spruce tissue culture

In order to develop more economic uses of lignin, greater knowledge regarding its native structure is required. This can inform the development of optimized extraction methods that preserve desired structural properties. Current extraction methods alter the polymeric structure of lignin, leading to a loss of valuable structural groups or the formation of new non-native ones. In this study, Norway spruce (Picea abies) tissue-cultured cells that produce lignin extracellularly in a suspension medium were employed. This system enables the investigation of unaltered native lignin, as no physicochemical extraction steps are required. For the first time, this culture was used to investigate the interactions between lignin and xylan, a secondary cell wall hemicellulose, and to study the importance of lignin-carbohydrate complexes (LCCs) on the polymerization and final structure of extracellular lignin (ECL). This has enabled us to study the impact of xylan on monolignol composition and structure of the final lignin polymer. We find that the addition of xylan to the solid culture medium accelerates cell growth and impacts the ratio of monolignols in the lignin. However, the presence of xylan in the lignin polymerization environment does not significantly alter the structural properties of lignin as analyzed by two-dimensional nuclear magnetic resonance (NMR) spectroscopy and size exclusion chromatography (SEC). Nevertheless, our data indicate that xylan can act as a nucleation point, leading to more rapid lignin polymerization, an important insight into biopolymer interactions during cell wall synthesis in wood. Lignin structure and interactions with a secondary cell wall hemicellulose were investigated in a model cell culture: we found that the polymerization and final structure of lignin are altered when the hemicellulose is present during cell growth and monolignol production. The physicochemical interactions between lignin and xylan partly define the extractability and utility of native lignin in high value applications, so this work has implications for lignin extraction as well as fundamental plant biology.

MicroRNA408 negatively regulates salt tolerance by affecting secondary cell wall development in maize

Although microRNA408 (miR408) is a highly conserved miRNA, the miR408 response to salt stress differs among plant species. Here, we show that miR408 transcripts are strongly repressed by salt stress and methyl viologen treatment in maize (Zea mays). Application of N, N1-dimethylthiourea partly relieved the NaCl-induced down-regulation of miR408. Transgenic maize overexpressing MIR408b is hypersensitive to salt stress. Overexpression of MIR408b enhanced the rate of net Na+ efflux, caused Na+ to locate in the inter-cellular space, reduced lignin accumulation, and reduced the number of cells in vascular bundles under salt stress. We further demonstrated that miR408 targets ZmLACCASE9 (ZmLAC9). Knockout of MIR408a or MIR408b or overexpression of ZmLAC9 increased the accumulation of lignin, thickened the walls of pavement cells, and improved salt tolerance of maize. Transcriptome profiles of the wild-type and MIR408b-overexpressing transgenic maize with or without salt stress indicated that miR408 negatively regulates the expression of cell wall biogenesis genes under salt conditions. These results indicate that miR408 negatively regulates salt tolerance by regulating secondary cell wall development in maize.

Tuning the Effect of Chitosan on the Electrochemical Responsiveness of Lignin Nanoparticles

Chitosan and lignin mixed nanoparticles were prepared by layer-by-layer and nanoprecipitation methodologies as responsive platforms for sustainable biosensors. The novel nanoparticles showed effective chemophysical and electrochemical properties dependent on the preparation methodology, molecular weight of chitosan, and type of lignin. HOMO-LUMO energy gap calculations suggested the presence of structure-activity relationships between the electrochemical responsiveness and the order and orientation of lignin aromatic subunits and chitosan chains in the nanodevices.

Application of Alkali Lignin and Spruce Sawdust for the Effective Removal of Reactive Dyes from Model Wastewater

Today, the emphasis is on environmentally friendly materials. Alkali lignin and spruce sawdust are suitable natural alternatives for removing dyes from wastewater. The main reason for using alkaline lignin as a sorbent is the recovery of waste black liquor from the paper industry. This work deals with removing dyes from wastewater using spruce sawdust and lignin at two different temperatures. The decolorization yields were calculated as the final values. Increasing the temperature during adsorption leads to higher decolorization yields, which may be due to the fact that some substances react only at elevated temperatures. The results of this research are useful for the treatment of industrial wastewater in paper mills, and the waste black liquor (alkaline lignin) can be used as a biosorbent.

ZmDRR206 Regulates Nutrient Accumulation in Endosperm through Its Role in Cell Wall Biogenesis during Maize Kernel Development

Dirigent proteins (DIRs) contribute to plant fitness by dynamically reorganizing the cell wall and/or by generating defense compounds during plant growth, development, and interactions with environmental stresses. ZmDRR206 is a maize DIR, it plays a role in maintaining cell wall integrity during seedling growth and defense response in maize, but its role in regulating maize kernel development is unclear. Association analysis of candidate genes indicated that the natural variations of ZmDRR206 were significantly associated with maize hundred-kernel weight (HKW). ZmDRR206 plays a dominant role in storage nutrient accumulation in endosperm during maize kernel development, ZmDRR206 overexpression resulted in small and shrunken maize kernel with significantly reduced starch content and significantly decreased HKW. Cytological characterization of the developing maize kernels revealed that ZmDRR206 overexpression induced dysfunctional basal endosperm transfer layer (BETL) cells, which were shorter with less wall ingrowth, and defense response was constitutively activated in developing maize kernel at 15 and 18 DAP by ZmDRR206 overexpression. The BETL-development-related genes and auxin signal-related genes were down-regulated, while cell wall biogenesis-related genes were up-regulated in developing BETL of the ZmDRR206-overexpressing kernel. Moreover, the developing ZmDRR206-overexpressing kernel had significantly reduced contents of the cell wall components such as cellulose and acid soluble lignin. These results suggest that ZmDRR206 may play a regulatory role in coordinating cell development, storage nutrient metabolism, and stress responses during maize kernel development through its role in cell wall biogenesis and defense response, and provides new insights into understanding the mechanisms of kernel development in maize.

The MADS-box gene EjAGL15 positively regulates lignin deposition in the flesh of loquat fruit during its storage

Introduction

Lignification of fruit flesh is a common physiological disorder that occurs during post-harvest storage, resulting in the deterioration of fruit quality. Lignin deposition in loquat fruit flesh occurs due to chilling injury or senescence, at temperatures around 0°C or 20°C, respectively. Despite extensive research on the molecular mechanisms underlying chilling-induced lignification, the key genes responsible for the lignification process during senescence in loquat fruit remain unknown. MADS-box genes, an evolutionarily conserved transcription factor family, have been suggested to play a role in regulating senescence. However, it is still unclear whether MADS-box genes can regulate the lignin deposition that arises from fruit senescence.

Methods

Both senescence- and chilling-induced flesh lignification were simulated by applying temperature treatments on loquat fruits. The flesh lignin content during the storage was measured. Transcriptomic, quantitative reverse transcription PCR and correlation analysis were employed to identify key MADS-box genes that may be involved in flesh lignification. The Dual-luciferase assay was utilized to identify the potential interactions between MADS-box members and genes in phenylpropanoid pathway.

Results and Discussion

The lignin content of the flesh samples treated at 20°C or 0°C increased during storage, but at different rates. Results from transcriptome analysis, quantitative reverse transcription PCR, and correlation analysis led us to identify a senescence-specific MADS-box gene, EjAGL15, which correlated positively with the variation in lignin content of loquat fruit. Luciferase assay results confirmed that EjAGL15 activated multiple lignin biosynthesis-related genes. Our findings suggest that EjAGL15 functions as a positive regulator of senescence-induced flesh lignification in loquat fruit.

Integrating biochemical and anatomical characterizations with transcriptome analysis to dissect superior stem strength of ZS11 (Brassica napus)

Stem lodging resistance is a serious problem impairing crop yield and quality. ZS11 is an adaptable and stable yielding rapeseed variety with excellent resistance to lodging. However, the mechanism regulating lodging resistance in ZS11 remains unclear. Here, we observed that high stem mechanical strength is the main factor determining the superior lodging resistance of ZS11 through a comparative biology study. Compared with 4D122, ZS11 has higher rind penetrometer resistance (RPR) and stem breaking strength (SBS) at flowering and silique stages. Anatomical analysis shows that ZS11 exhibits thicker xylem layers and denser interfascicular fibrocytes. Analysis of cell wall components suggests that ZS11 possessed more lignin and cellulose during stem secondary development. By comparative transcriptome analysis, we reveal a relatively higher expression of genes required for S-adenosylmethionine (SAM) synthesis, and several key genes (4-COUMATATE-CoA LIGASE, CINNAMOYL-CoA REDUCTASE, CAFFEATE O-METHYLTRANSFERASE, PEROXIDASE) involved in lignin synthesis pathway in ZS11, which support an enhanced lignin biosynthesis ability in the ZS11 stem. Moreover, the difference in cellulose may relate to the significant enrichment of DEGs associated with microtubule-related process and cytoskeleton organization at the flowering stage. Protein interaction network analysis indicate that the preferential expression of several genes, such as LONESOME HIGHWAY (LHW), DNA BINDING WITH ONE FINGERS (DOFs), WUSCHEL HOMEOBOX RELATED 4 (WOX4), are related to vascular development and contribute to denser and thicker lignified cell layers in ZS11. Taken together, our results provide insights into the physiological and molecular regulatory basis for the formation of stem lodging resistance in ZS11, which will greatly promote the application of this superior trait in rapeseed breeding.