Lignin Pathway Research Articles

Chronological events unfolding the vegetative and floral phenology of apical bud in Crocus sativus.

Saffron (Crocus sativus L.) is an infertile perennial geophyte considered the most expensive spice in the world. Seasonal fluctuations and climate change have significant impact on the growth, development, and yield of saffron stigma, which is the economically valued part of plant. The stigma being part of the flower, the knowledge of phenotypic transition from dormant apical bud up to flowering is vital, yet, not explored properly. The complexity of flowering in C. sativus further accentuates by the lack of clear demarcation between flowering and non-flowering corms in terms of weight and sizes, as small corms are known to be vegetative only, while large ones produce flower. Therefore, chronological phenotyping on a weekly and quarterly basis of apical shoot and flowering primordia between June and October was carried out to understand the organogenesis sequentially. In large corms, the stamen was the first floral organ to initiate followed by the formation of tepal from the base of the stamen. The plants exhibited both synanthous and hysteranthous flowering. Untargeted metabolome analysis of dormant apical bud just before dormancy break from flowering buds from large corms as well as non-flowering buds from small corms identified the presence of many differentially accumulated metabolites including sphingosine and meglutol. Key metabolites such as phytosphingosine, 3-hydroxy-3-methyl glutaric acid, 3-acetamidopropanal, 6-hydroxykynurenic acid, D-serine, and 1-D-myo-inositol 3-phosphate were also detected having associated with isoprenoid biosynthesis, lignin pathway regulation, and carbohydrate metabolism that participates in flowering. The integration of morphological, histological, and metabolomic data offers a comprehensive view of the flowering process that can be utilised in future biotechnological interventions in C. sativus.

Enhanced humification attributed by the integration of Fenton reagent and oxalic acid during a co-composting of swine manure and corn straw: Impacts and the possible mechanisms

To illustrate the role and mechanism of using oxalic acid (OA) and Fenton reagent to enhance carbon transformation and humification in the co-composting of swine manure and corn straw, four different treatments, SW1 (Control), SW2 (Fenton reagent), SW3 (10 % OA), and SW4 (Fenton reagent + 10 % OA) were set up for an 80-day pilot-scale composting. Compared with the Fenton pretreatment, the contents of Fe (II) and hydroxyl radicals (·OH) in the SW4 treatment increased by 20.25 %-54.55 % and 6.39 %-71.00 %, respectively. This confirmed the role of OA in protecting Fe (II) and maintaining the generation of ·OH during the composting. Compared with Control, Fenton-like reagent amendment facilitated decomposition of dissolved organic carbon and total organic matter by 20.53 % and 25.37 %, respectively, which led to a higher content of humic substances (141.81 mg/g) and a higher degree of polymerization (3.51) in SW4. Among all, the dissolved organic carbon in the compost substrate of SW4 treatment showed the highest level of aromatization and more refractory organic matter decomposition. The compact microbial co-occurrence network analysis exhibited the high-metabolic activity in Fenton-like treatment (SW4). Therefore, the probable mechanism of humification facilitation by Fenton-like reagent amendment in co-composting could be controlled by several processes: 1) generation of ·OH for facilitating the decomposition of organic matter, 2) disintegration of refractory lignocellulose substances by promoting the lignin pathway of humification, and 3) increasing the quantity and activity of microbes (i.e., Proteobacteria, Actinobacteriota, Chloroflexi, Ascomycota and Basidiomycota) involved in humification. This study provided a profound understanding of Fenton-like reagent amendments in co-composting of agricultural solid wastes and proposes a solution for enhancing the humification degree of compost products for agricultural use.

Arbuscular mycorrhizal fungi improve the disease resistance of Lycium barbarum to root rot by activating phenylpropane metabolism.

Root rot is one of the common diseases of Lycium barbarum. Pathogens can cause devastating disasters to plants after infecting host plants. This study investigated the effect of arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices inoculation on phenylpropane metabolism in L. barbarum and evaluated its resistance to root rot. The experiment was set up with AMF inoculation treatments (inoculated or not) and root rot pathogen-Fusarium solani inoculation treatments (inoculated or not). The results showed that AMF was able to form a symbiosis with the root system of L. barbarum, thereby promoting plant growth significantly and increasing plants' resistance to disease stress. The plant height of AMF-colonized L. barbarum increased by 24.83% compared to non-inoculated diseased plants. After inoculation with AMF, the plant defense response induced by pathogen infection was stronger. When the enzyme activity of the leaves reached the maximum after the onset of mycorrhizal L. barbarum, phenylalanine ammonia-lyase, cinnamic acid-4-hydroxylase, and 4-coumaric acid-CoA ligase increased by 3.67%, 31.47%, and 13.61%, respectively, compared with the non-inoculated diseased plants. The products related to the lignin pathway and flavonoid pathway downstream of phenylpropane metabolism such as lignin and flavonoids were also significantly increased by 141.65% and 44.61% compared to nonmycorrhizal diseased plants. The activities of chitinase and β-1,3-glucanase increased by 36.00% and 57.96%, respectively. The contents of salicylic acid and jasmonic acid were also 17.7% and 31.63% higher than those of nonmycorrhizal plants in the early stage of plant growth, respectively. The results indicated that AMF significantly promoted plant growth and enhanced disease resistance by increasing enzyme activities and the production of lignin and flavonoids.

Study on detailed reaction pathways of sulfur-containing alkali lignin during supercritical water gasification for hydrogen production

This work was focused on the evolution process of alkali lignin with a macromolecular structure in supercritical water gasification reactions. Using Quantum chemistry calculations and molecular dynamics simulations, the effects of different factors on the reaction process were studied, and the detailed pathways of main products were obtained. The results indicate that the presence of sulfur significantly inhibits the pyrolysis behavior of alkali lignin macromolecular structures. Sulfur significantly impacts the morphology of the intermediate molecular fragments of products containing 5–10 carbon atoms. Sulfur also has a significant inhibitory effect on the ring opening reaction of the benzene ring. Still, its effect on the final gas product distribution is not significant from a microscopic perspective. In addition, high temperature has a significant impact on improving the gasification efficiency of alkali lignin, while the scale of the reaction system has no significant effect on the distribution of gas products. This study will provide theoretical guidance for further improving the supercritical water gasification efficiency of lignin.

Genome-Wide Identification, Evolution, and Expression Analysis of the DIR Gene Family in Schima superba.

Schima superba, commonly known as the Chinese guger tree, is highly adaptable and tolerant of poor soil conditions. It is one of the primary species forming the evergreen broad-leaved forests in southern China. Dirigent proteins (DIRs) play crucial roles in the synthesis of plant lignin and lignans, secondary metabolism, and response to adversity stress. However, research on the DIR gene family in S. superba is currently limited. This study identified 24 SsDIR genes, categorizing them into three subfamilies. These genes are unevenly distributed across 13 chromosomes, with 83% being intronless. Collinearity analysis indicated that tandem duplication played a more significant role in the expansion of the gene family compared to segmental duplication. Additionally, we analyzed the expression patterns of SsDIRs in different tissues of S. superba. The SsDIR genes exhibited distinct expression patterns across various tissues, with most being specifically expressed in the roots. Further screening identified SsDIR genes that may regulate drought stress, with many showing differential expression under drought stress conditions. In the promoter regions of SsDIRs, various cis-regulatory elements involved in developmental regulation, hormone response, and stress response were identified, which may be closely related to their diverse regulatory functions. This study will contribute to the further functional identification of SsDIR genes, providing insights into the biosynthetic pathways of lignin and lignans and the mechanisms of plant stress resistance.

Passion fruit HD-ZIP genes: Characterization, expression variance, and overexpression PeHB31 enhanced drought tolerance via lignin pathway

The HD-ZIP (homeodomain-leucine zipper) genes hold significant importance in transcriptional regulation, especially in plant development and responses to abiotic stresses. However, a comprehensive study targeting HD-ZIP family members in passion fruit has been absent. In our current research, 34 HD-ZIP family members (PeHBs) were identified by bioinformatics analysis. Transcriptome analysis revealed that PeHBs exhibited distinct expression patterns when subjected to the four different abiotic stresses, and significant differential expression of PeHBs was also found among the three developmental stages of the fruit and between the purple and yellow genotype passion fruit leaves. An integrated metabolome and transcriptome analysis further revealed that the HD-ZIP III class gene PeHB31 (homologous to ATHB8), was co-upexpressed with lignans in yellow fruit P. edulis (commonly used as a resistance rootstock) when compared to purple fruit P. edulis. The transformation of Arabidopsis and yeast with the PeHB31 gene showed an enhancement in their capacity to withstand drought conditions. Notably, the transgenic Arabidopsis plants exhibited an increase in lignin content within the vascular tissues of their stems. This research lays the groundwork for future studies on the control mechanisms of lignin biosynthesis by HD-ZIP genes (especially HD-ZIP classes III and I) involved in drought tolerance.

Combined use of versatile peroxidase and aryl alcohol oxidase of Pleurotus eryngii to decolorize melanin on the skin

Melanin plays an important role in protecting skin cells from harmful UV radiation, but its uneven pigmentation in the skin sometimes demands cosmetic resolution. As a safe and effective way of evening the skin tone, enzymatic decolorization of melanin at the stratum corneum has been proposed. In this regard, the use of lignin peroxidase, in the presence of hydrogen peroxide and veratryl alcohol, an electron mediator, has been explored. Here, we first show that versatile peroxidase (VP) and aryl alcohol oxidase (AAO) purified from the Pleurotus eryngii liquid culture can be used to decolorize melanin without exogenous hydrogen peroxide. This resembles the oxidative degradation pathway of lignin in nature; AAO generates hydrogen peroxide from veratryl alcohol, and VP utilizes generated hydrogen peroxide while using veratryl alcohol as a mediator. We further explored the use of POX_Pe, the crude peroxidase preparation of the Pleurotus eryngii liquid culture, for melanin decolorization because of its better stability. Using POX_Pe and veratryl alcohol, over 60 % of melanin decolorization was obtained in 1 h in the absence of exogenous hydrogen peroxide addition. Furthermore, POX_Pe could decolorize melanin in a 3D human pigmented epidermis model, demonstrating its possible applications in cosmetics.

PpSAUR5 promotes plant growth by regulating lignin and hormone pathways.

Peach (Prunus persica) has a high nutritional and economic value. However, its overgrowth can lead to yield loss. Regulating the growth of peach trees is challenging. The small auxin-up RNA (SAUR) gene family is the largest family of auxin-responsive genes, which play important roles in plant growth and development. However, members of this gene family are rarely reported in peach. In this study, we measured leaf area, chlorophyll and lignin content to detect the role of PpSAUR5 on growth through transgenic Arabidopsis. PpSAUR5 responds to auxin and gibberellin, promoting and inhibiting the synthesis of gibberellin and auxin, respectively. The heterologous transformation of PpSAUR5 in Arabidopsis led to enhanced growth of leaves and siliques, lightening of leaf color, decrease in chlorophyll content, increase in lignin content, abnormalities in the floral organs, and distortion of the inflorescence axis. Transcriptome data analysis of PpSAUR5 overexpression and wild-type lines revealed 854 differentially expressed genes (DEGs). GO and KEGG analyses showed that the DEGs were primarily involved in biological processes, such as cellular processes, metabolic processes, response to stimuli, and catalytic activity. These genes were mainly enriched in pathways, such as phenylalanine biosynthesis, phytohormone signaling, and MAPK signaling. In summary, these results suggested that PpSAUR5 might regulate tree vigor by modulating the synthesis of auxin and gibberellin. Future studies can use PpSAUR5 as a candidate gene to elucidate the potential regulatory mechanisms underlying peach tree vigor.

Selection of stable housekeeping genes for qPCR in biotic and abiotic stressed jute and their application in lignin pathway analysis

This is a comprehensive examination of housekeeping gene (HKG) expression in jute (Corchorus sp.), essential for reliable qRT-PCR studies. Jute is the most abundant and vital source of bast (phloem) fibres that have diverse domestic and industrial applications. The functional analysis of genes in jute is crucial for enhancing its commercial potential and value. We specifically focused on 24 HKGs, including nine previously recommended HKGs for jute. We focused the investigation on the only two commercially cultivated species of jute—C. capsularis and C. olitorius. The jute plants were subjected to nine abiotic stresses: osmotic, salinity, low temperature, high temperature, waterlogging, ABA stress hormone, glyphosate herbicide, and heavy metals (copper and cadmium), along with a biotic stress condition—Macrophomina phaseolina (fungal) infection. After rigorous analyses using the ΔCt method, BestKeeper, geNorm, NormFinder, and RefFinder, we identified ubiquitin1 (UBI) and beta-tubulin (BTUB) as the most stable HKGs for both the jute species under various stress conditions. The gene stability of UBI and BTUB was assessed in different jute cultivars, tissues, at different developmental stages, and PCR conditions. As a case study, we investigated eight genes involved in the jute lignin pathway in a low-lignin fibre-producing white jute mutant cultivar—dlpf—compared to its control cultivar, JRC212. Our findings revealed low expression of the three genes- CcCCoAoMT2, CcC4H1, and CcCAD7 in the dlpf cultivar, promising a potential for developing low-lignin jute varieties to meet long-standing industrial demands. The jute HKG expressions under various stress conditions establish a foundation for future research for crop improvement.

Transcriptomic and physiological analysis provide new insight into seed shattering mechanism in Pennisetum alopecuroides 'Liqiu'.

Through the histological, physiological, and transcriptome-level identification of the abscission zoneof Pennisetum alopecuroides 'Liqiu',we explored the structure and the genes related to seed shattering,ultimately revealing the regulatory network of seed shattering in P. alopecuroides. Pennisetum alopecuroides is one of the most representative ornamental grass species of Pennisetum genus. It has unique inflorescence, elegant appearance, and strong stress tolerance. However, the shattering of seeds not only reduces the ornamental effect, but also hinders the seed production. In order to understand the potential mechanisms of seed shattering in P. alopecuroides, we conducted morphological, histological, physiological, and transcriptomic analyses on P. alopecuroides cv. 'Liqiu'. According to histological findings, the seed shattering of 'Liqiu' was determined by the abscission zone at the base of the pedicel. Correlation analysis showed that seed shattering was significantly correlated with cellulase, lignin, auxin, gibberellin, cytokinin and jasmonic acid. Through a combination of histological and physiological analyses, we observed the accumulation of cellulase and lignin during 'Liqiu' seed abscission. We used PacBio full-length transcriptome sequencing (SMRT) combined with next-generation sequencing (NGS) transcriptome technology to improve the transcriptome data of 'Liqiu'. Transcriptomics further identified many differential genes involved in cellulase, lignin and plant hormone-related pathways. This study will provide new insights into the research on the shattering mechanism of P. alopecuroides.

A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds.

Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.

Response of lignin and flavonoid metabolic pathways in Capsicum annuum to drought and waterlogging stresses

Water stress is a critical factor limiting the growth and development of Capsicum annuum. Flavonoids and lignin are important secondary metabolites that serve as signaling molecules in plant stress responses. However, the effects and regulatory mechanisms of lignin and flavonoids under water stress in Capsicum annuum remain unknown. The present study focused on the effects of drought and waterlogging stress on the morphology, hydrogen peroxide, and relative chlorophyll (SPAD), as well as enzyme activities, metabolite contents, and gene expression related to lignin and flavonoid metabolic pathways in Capsicum annuum. The results showed that drought and waterlogging stresses on the Capsicum annuum variety ‘Shuyu2’ significantly reduced plant height, stem thickness, and single-fruit weight, and increased fruit shape coefficients. Drought stress increased H2O2 and SPAD content, enhanced the activity levels of metabolic enzymes (phenylalanine deaminase, cinnamate 4-hydroxylase, coenzyme A ligase, peroxidase, and polyphenol oxidase), and up-regulated the expression of related genes, phenylalanine deaminase (PAL), trans-cinnamate monooxygenase (C4H), chalcone isomerase (CHI), and mangiferyl hydroxycinnamoyltransferase (HCT), while also promoting the accumulation of metabolites (total phenolics, flavonoids, and lignin) that have a restorative effect on drought stress. The continuous accumulation of H2O2 and the increase and then decrease in SPAD under waterlogging stress was also observed. Waterlogging stress also enhanced the activities of the above-mentioned metabolic enzymes, but the related genes were selectively down-regulated, e.g., C4H, 4CL, and peroxidase (POD), which resulted in the inhibition of the synthesis of lignin, flavonoids, and total phenols. These results indicate that the Capsicum annuum variety ‘Shuyu2’ is a drought-tolerant, waterlogging-sensitive variety. Meanwhile, the lignin and flavonoid pathway is a key pathway in response to drought stress in Capsicum annuum, which improves the theory of stress tolerance breeding in Capsicum annuum.

Study on the mechanism of lignin and lignin-carbohydrate complex hydrolysis under alkaline conditions by density functional theory

Lignin hydrolyzes during alkali-heat pretreatment of lignocellulose, due to the cleavage of covalent linkages between lignin and lignin-carbohydrate complex. Various structure of lignin monomers are responsible of the complicated hydrolysis mechanism of lignin and lignin-carbohydrate complex. This study used density functional theory to reveal the hydrolysis mechanism of lignin with various substituents and lignin-carbohydrates complex with different linkages. The results indicated that the SN2 reaction was observed to take place in the lignin. Methoxy groups and methyl group had an insignificant influence on hydrolysis reaction pathway of lignin, whereas the presence of a methyl group on the α-carbon atom had a hindering effect on the nucleophilic attack during alkaline pretreatment. The lignin-carbohydrate complex with different linkage showed a significant difference in hydrolysis reaction pathway. Additionally, the reaction energy barrier of ester bond hydrolysis was lowest among the hydrolysis of ester bond, phenyl glycosidic bond, benzyl ether bond, γ-ester bond, coumarin ester bond and acetal bond under alkaline condition. This study provides valuable insights into the process control, reactor design, and performance enhancement for lignocellulose pretreatment.

Hydrogen-transfer strategy in lignin refinery: Towards sustainable and versatile value-added biochemicals.

Lignin, the most prevalent natural source of polyphenols on Earth, offers substantial possibilities for the conversion into aromatic compounds, which is critical for attaining sustainability and carbon neutrality. The hydrogen-transfer method has garnered significant interest owing to its environmental compatibility and economic viability. The efficacy of this approach is contingent upon the careful selection of catalytic and hydrogen-donating systems that decisively affect the yield and selectivity of the monomeric products resulting from lignin degradation. This paper highlights the hydrogen-transfer technique in lignin refinery, with a specific focus on the influence of hydrogen donors on the depolymerization pathways of lignin. It delineates the correlation between the structure and activity of catalytic hydrogen-transfer arrangements and the gamut of lignin-derived biochemicals, utilizing data from lignin model compounds, separated lignin, and lignocellulosic biomass. Additionally, the paper delves into the advantages and future directions of employing the hydrogen-transfer approach for lignin conversion. In essence, this concept investigation illuminates the efficacy of the hydrogen-transfer paradigm in lignin valorization, offering key insights and strategic directives to maximize lignin's value sustainably.

Transforming lignin into value-added products: Perspectives on lignin chemistry, lignin-based biocomposites, and pathways for augmenting ligninolytic enzyme production

Transforming lignin into value-added products: Perspectives on lignin chemistry, lignin-based biocomposites, and pathways for augmenting ligninolytic enzyme production

Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance

BackgroundWhiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated.ResultsWhitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246’s response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava’s hormone-responsive genes showed striking divergence in expression.ConclusionsThis study provides the first characterization of cassava’s global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.

Identification of the Key Genes Involved in Proline-Mediated Modification of Cell Wall Components in Rice Seedlings under Trivalent Chromium Exposure.

Chromium (Cr) toxicity exerts a detrimental effect on various physiological, biochemical, and molecular attributes of plants including the structure and functions of cell walls. On the other hand, the exogenous application of proline (Pro) is a beneficial strategy to overcome Cr toxicity. Therefore, it is a novel strategy to find the key genes associated with cell wall composition in rice under trivalent Cr with/without Pro application. A total of 203 genes were activated in the four cell wall biosynthesis pathways under chromium stress, namely cellulose (60), hemicellulose (57), lignin (35), and pectin (51). Based on the expression abundance of microarrays, the number of differentially expressed genes, and the expression level of genes, the lignin pathway was a crucial pathway in response to Cr treatments, followed by the cellulose pathway. Through the estimation of gene expression variation factors between 'Cr' and 'Cr+Pro' treatments, OsUGP1, OsBGLU24, OsBGLU29, OsBGLU33, OsBMY1, and OsBMY2 in the cellulose pathway; OsXTH9, OsXTH10, OsXTH16, OsGAUT3, OsGAUT19, OsGAUT28, OsXTH1, OsGAUT12, and OsGAUT21 in the hemicellulose pathway; OsPAL3, OsPAL3, OsPOX1, and OsPRX77 in the lignin pathway; and OsPME25, OsPGL27, OsPME26, OsPGL9, and OsPLL12 in the pectin pathway are the key genes involved in cell wall modification during Cr exposure with exogenous Pro application. The Pro-mediated activation of these genes could be crucial players in modifying the cell wall structure and composition of rice plants under Cr stress, which needs to be further clarified.

Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses

Vascular plants direct large amounts of carbon to produce the aromatic amino acid phenylalanine to support the production of lignin and other phenylpropanoids. Uniquely, grasses, which include many major crops, can synthesize lignin and phenylpropanoids from both phenylalanine and tyrosine. However, how grasses regulate aromatic amino acid biosynthesis to feed this dual lignin pathway is unknown. Here we show, by stable-isotope labeling, that grasses produce tyrosine >10-times faster than Arabidopsis without compromising phenylalanine biosynthesis. Detailed in vitro enzyme characterization and combinatorial in planta expression uncovered that coordinated expression of specific enzyme isoforms at the entry and exit steps of the aromatic amino acid pathway enables grasses to maintain high production of both tyrosine and phenylalanine, the precursors of the dual lignin pathway. These findings highlight the complex regulation of plant aromatic amino acid biosynthesis and provide novel genetic tools to engineer the interface of primary and specialized metabolism in plants.

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources.

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.

Evolution and Analysis of Caffeic Acid Transferase (COMT) in Seed Plants.

Caffeic acid transferase (COMT) is a key enzyme in the lignin and melatonin synthesis pathways and plays an important role in plant growth and development. All seed plants have two characteristics: they have vascular tissues, phloem, and xylem, and they can produce and reproduce seeds. In order to understand the distribution and evolution of COMTs in seed plants, we performed physicochemical property analysis, subcellular localization, phylogenetic analysis, conserved motif analysis, and protein interaction network analysis of 44 COMT homologs from 26 seed plants through in silico. The results showed that in seed plants, the structure of COMT genes tends to be stable in different plant taxa, while the relationship between the chromosomal positions of different COMT genes in the same plant was more intricate. The conserved distribution of COMT in seed plants reflected its highly specialized function.