Rewriting the lignin roadmap

Major facilitator family transporters specifically enhance caffeyl alcohol uptake during C-lignin biosynthesis

The mode of transport of lignin monomers to the sites of polymerization in the apoplast remains controversial. C-Lignin is a recently discovered form of lignin found in some seed coats that is composed exclusively of units derived from caffeyl alcohol. RNA-seq and proteome analyses identified a number of transporters co-expressed with C-lignin deposition in the seed coat of Cleome hassleriana. Cloning and influx/efflux analysis assays in yeast identified two low-affinity transporters, ChPLT3 and ChSUC1, that were active with caffeyl alcohol but not with the classical monolignols p-coumaryl, coniferyl, and sinapyl alcohols, consistent with molecular modeling and docking studies. Expression of ChPLT3 in Arabidopsis seedlings enhanced root growth in the presence of caffeyl alcohol, and expression of ChPLT3 and ChSUC1 correlated with lignin C-unit content in hairy roots of Medicago truncatula. We present a model, consistent with phylogenetic and evolutionary considerations, whereby passive caffeyl alcohol transport may be supplemented by hitchhiking on secondary active transporters to ensure the synthesis of C-lignin, and inhibition of synthesis of G-lignin, in the apoplast.

Lignin and Nanolignin: Next-Generation Sustainable Materials for Water Treatment

Water scarcity, contamination, and lack of sanitation are global issues that require innovations in chemistry, engineering, and materials science. To tackle the challenge of providing high-quality drinking water for a growing population, we need to develop high-performance and multifunctional materials to treat water on both small and large scales. As modern society and science prioritize more sustainable engineering practices, water treatment processes will need to use materials produced from sustainable resources via green chemical routes, combining multiple advanced properties such as high surface area and great affinity for contaminants. Lignin, one of the major components of plants and an abundant byproduct of the cellulose and bioethanol industries, offers a cost-effective and scalable platform for developing such materials, with a wide range of physicochemical properties that can be tailored to improve their performance for target water treatment applications. This review aims to bridge the current gap in the literature by exploring the use of lignin, both as solid bulk or solubilized macromolecules and nanolignin as multifunctional (nano)materials for sustainable water treatment processes. We address the application of lignin-based macro-, micro-, and nanostructured materials in adsorption, catalysis, flocculation, membrane filtration processes, and antimicrobial coatings and composites. Throughout the exploration of recent progress and trends in this field, we emphasize the importance of integrating principles of green chemistry and materials sustainability to advance sustainable water treatment technologies.

Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit

The Chinese white pear (Pyrus bretschneideri) is an economically significant fruit crop worldwide. Previous versions of the P. bretschneideri genome assembly contain numerous gaps and unanchored genetic regions. Here, we generated two high-quality, gap-free genome assemblies for 'Dangshansu' (DS; 503.92 Mb) and 'Lianglizaosu' (ZS; 509.01 Mb), each anchored to 17 chromosomes, achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%. Our genome-wide association studies explored the associations between genetic variations and stone cell traits, revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene, designated PbdsZF. Through genetic transformation, we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation, as it transcriptionally activates multiple genes involved in these processes. By binding to the CT-rich motifs CT1 (CTTTTTTCT) and CT2 (CTCTTTTT), PbdsZF significantly influences the transcription of genes essential for lignin production, underscoring its regulatory importance in plant lignin metabolism. Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation, thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.

Chemical Synthesis of Monolignols: Traditional Methods, Recent Advances, and Future Challenges in Sustainable Processes

Monolignols represent pivotal alcohol-based constituents in lignin synthesis, playing indispensable roles in plant growth and development with profound implications for industries reliant on wood and paper. Monolignols and their derivates have multiple applications in several industries. Monolignols exhibit antioxidant activity due to their ability to donate hydrogen atoms or electrons to neutralize free radicals, thus preventing oxidative stress and damage to cells. Characterized by their alcohol functionalities, monolignols present three main forms: p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol. In nature, particularly in plants, monolignols with geometry (E) predominate over their Z counterparts. The methods for obtaining the three canonical monolignols, two less-common monolignols, and a monolignol analogue are addressed to present an overview of these phenol-based compounds, particularly from a synthetic standpoint. A SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis is used to explain the advantages and disadvantages of synthesizing monolignols, key alcohol-containing raw materials with enormous significance in both plant biology and industrial applications, using bench chemical methods. The uniqueness of this work is that it provides an overview of the synthetic pathways of monolignols to assist researchers in pharmaceutical and biological fields in selecting an appropriate procedure for the preparation of their lignin models. Moreover, we aim to inspire scientists, particularly chemists, to develop more sustainable synthetic protocols for monolignols.

Molecular mechanisms underlying gene regulatory variation of maize metabolic traits

Variation in gene expression levels is pervasive among individuals and races or varieties, and has substantial agronomic consequences, for example, by contributing to hybrid vigor. Gene expression level variation results from mutations in regulatory sequences (cis) and/or transcription factor (TF) activity (trans), but the mechanisms underlying cis- and/or trans-regulatory variation of complex phenotypes remain largely unknown. Here, we investigated gene expression variation mechanisms underlying the differential accumulation of the insecticidal compounds maysin and chlorogenic acid in silks of widely used maize (Zea mays) inbreds, B73 and A632. By combining transcriptomics and cistromics, we identified 1,338 silk direct targets of the maize R2R3-MYB TF Pericarp color1 (P1), consistent with it being a regulator of maysin and chlorogenic acid biosynthesis. Among these P1 targets, 464 showed allele-specific expression (ASE) between B73 and A632 silks. Allelic DNA-affinity purification sequencing identified 34 examples in which P1 allelic specific binding (ASB) correlated with cis-expression variation. From previous yeast one-hybrid studies, we identified 9 TFs potentially implicated in the control of P1 targets, with ASB to 83 out of 464 ASE genes (cis) and differential expression of 4 out of 9 TFs between B73 and A632 silks (trans). These results provide a molecular framework for understanding universal mechanisms underlying natural variation of gene expression levels, and how the regulation of metabolic diversity is established.

Whole-Cell Bioconversion Systems for Efficient Synthesis of Monolignols from L-Tyrosine in Escherichia coli

Monolignols and their derivatives exhibit various pharmaceutical and physiological characteristics, such as antioxidant and anti-inflammatory properties. However, they remain difficult to synthesize. In this study, we engineered several whole-cell bioconversion systems with carboxylate reductase (CAR)-mediated pathways for efficient synthesis of p-coumaryl, caffeyl, and coniferyl alcohols from l-tyrosine in Escherichia coli BL21 (DE3). By overexpressing the l-tyrosine ammonia lyase from Flavobacterium johnsoniae (FjTAL), carboxylate reductase from Segniliparus rugosus (SruCAR), alcohol dehydrogenase YqhD and hydroxylase HpaBC from E. coli, and caffeate 3-O-methyltransferase (COMT) from Arabidopsis thaliana, three enzyme cascades FjTAL-SruCAR-YqhD, FjTAL-SruCAR-YqhD-HpaBC, and FjTAL-SruCAR-YqhD-HpaBC-COMT were constructed to produce 1028.5 mg/L p-coumaryl alcohol, 1015.3 mg/L caffeyl alcohol, and 411.4 mg/L coniferyl alcohol from 1500, 1500, and 1000 mg/L l-tyrosine, with productivities of 257.1, 203.1, and 82.3 mg/L/h, respectively. This work provides an efficient strategy for the biosynthesis of p-coumaryl, caffeyl, and coniferyl alcohols from l-tyrosine.

Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining

Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations. Recent advances in our understanding of lignin biosynthesis have shown that lignin structure is extremely diverse and potentially tunable, while simultaneous developments in lignin refining have resulted in the development of several processes that are more agnostic to lignin composition. Here, we review the interface between in planta lignin design and lignin processing and discuss the advances necessary for lignin valorization to become a feature of advanced biorefining.

Bioproduction of methylated phenylpropenes and isoeugenol in Escherichia coli

Phenylpropenes are a class of natural products that are synthesised by a vast range of plant species and hold considerable promise in the flavour and fragrance industries. Many in vitro studies have been carried out to elucidate and characterise the enzymes responsible for the production of these volatile compounds. However, there is a scarcity of studies demonstrating the in vivo production of phenylpropenes in microbial cell factories. In this study, we engineered Escherichia coli to produce methylchavicol, methyleugenol and isoeugenol from their respective phenylacrylic acid precursors. We achieved this by extending and modifying a previously optimised heterologous pathway for the biosynthesis of chavicol and eugenol. We explored the potential of six S-adenosyl l-methionine (SAM)-dependent O-methyltransferases to produce methylchavicol and methyleugenol from chavicol and eugenol, respectively. Additionally, we examined two isoeugenol synthases for the production of isoeugenol from coniferyl acetate. The best-performing strains in this study were able to achieve titres of 13 mg L-1 methylchavicol, 59 mg L-1 methyleugenol and 361 mg L-1 isoeugenol after feeding with their appropriate phenylacrylic acid substrates. We were able to further increase the methyleugenol titre to 117 mg L-1 by supplementation with methionine to facilitate SAM recycling. Moreover, we report the biosynthesis of methylchavicol and methyleugenol from l-tyrosine through pathways involving six and eight enzymatic steps, respectively.

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

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

Characterization of sugarcane mutants developed through gamma irradiations for their lignin content and caffeic acid-O-methyl transferase (COMT) gene mutations

PURPOSE

Bagasse, the residue left after extracting juice from sugarcane stalks, is rich in lignocellulosic biomass. The lignin present in this plant biomass is the key factor that hinders the efficient extraction of ethanol from the bagasse. In the current study, γ-irradiated sugarcane mutants were evaluated for variation in lignin content and its corresponding caffeic acid-O-methyl transferase (COMT) gene.

MATERIALS AND METHODS

The acetyl bromide method was used to estimate lignin content in sugarcane mutants. PCR-based cloning of the COMT gene was performed in low lignin mutants as well as control plants in E. coli (strain DH5α) to understand the mechanism of variation at the molecular level. The Sanger sequencing for cloned gene was performed to check variation in gene sequence.

RESULTS

In comparison to the control (21.5%), the mutant plants' lignin content ranged from 13 to 28%. The Sanger sequencing revealed approximately the same length of the gene from mutants as well as a control plant. In comparison to the reference gene, the mutated gene showed SNPs and indels in different regions, which may have an impact on lignin content.

CONCLUSIONS

Therefore, γ-irradiated mutagenesis is an acceptable approach to develop novel mutants of sugarcane with low lignin content to enhance bioethanol production from waste material using bioprocess technology.

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.

Synthesis and Applications of Hybrid Polymer Networks Based on Renewable Natural Macromolecules

Macromolecules obtained from renewable natural sources are gaining increasing attention as components for a vast variety of sustainable polymer-based materials. Natural raw materials can facilitate continuous-flow production due to their year-round availability and short replenishment period. They also open new opportunities for chemists and biologists to design and create "bioreplacement" and "bioadvantaged" polymers, where complex structures produced by nature are being modified, upgraded, and utilized to create novel materials. Bio-based macromonomers are expected not only to compete with but to replace some petroleum-based analogs, as well. The development of novel sustainable materials is an ongoing and very dynamic process. There are multiple strategies for transforming natural macromolecules into sophisticated value-added products. Some methods include chemical modification of macromolecules, while others include blending several components into one new system. One of the most promising approaches for incorporating renewable macromolecules into new products is the synthesis of hybrid networks based on one or more natural components. Each one has unique characteristics, so its incorporation into a network brings new sustainable materials with properties that can be tuned according to their end-use. This article reviews the current state-of-the-art and future potential of renewable natural macromolecules as sustainable building blocks for the synthesis and use of hybrid polymer networks. The most recent advancements and applications that involve polymers, such as cellulose, chitin, alginic acid, gellan gum, lignin, and their derivatives, are discussed.

Modification of lignin composition by ectopic expressing wheat TaF5H1 led to decreased salt tolerance in transgenic Arabidopsis plants

Lignin is an important cell wall component that provides plants with mechanical support and improved tolerance to pathogen attacks. Previous studies have shown that plants rich in S-lignin content or with a higher S/G ratio always exhibit higher efficiency in the utilization of lignocellulosic biomass. Ferulate 5-hydroxylase, or coniferaldehyde 5-hydroxylase (F5H, or CAld5H), is the critical enzyme in syringyl lignin biosynthesis. Some F5Hs have been characterized in several plant species, e.g., Arabidopsis, rice, and poplar. However, information about F5Hs in wheat remains unclear. In this study, a wheat F5H gene, TaF5H1, together with its native promoter (pTaF5H1), was functionally characterized in transgenic Arabidopsis. Gus staining results showed that TaF5H1 could be expressed predominantly in the highly lignified tissues in transgenic Arabidopsis plants carrying pTaF5H1:Gus. qRT-PCR results showed that TaF5H1 was significantly inhibited by NaCl treatment. Ectopic expression of TaF5H1 driven by pTaF5H1 (i.e., pTaF5H1:TaF5H1) could increase the biomass yield, S-lignin content, and S/G ratio in transgenic Arabidopsis plants, which could also restore the traces of S-lignin in fah1-2, the Arabidopsis F5H mutant, to an even higher level than the wild type (WT), suggesting that TaF5H1 is a critical enzyme in S lignin biosynthesis, and pTaF5H1:TaF5H1 module has potential in the manipulation of S-lignin composition without any compromise on the biomass yield. However, expression of pTaF5H1:TaF5H1 also led to decreased salt tolerance compared with the WT. RNA-seq analysis showed that many stress-responsive genes and genes responsible for the biosynthesis of cell walls were differentially expressed between the seedlings harboring pTaF5H1:TaF5H1 and the WT, hinting that manipulation of the cell wall components targeting F5H may also affect the stress adaptability of the modified plants due to the interference to the cell wall integrity. In summary, this study demonstrated that the wheat pTaF5H1: TaF5H1 cassette has the potential to modulate S-lignin composition without any compromise in biomass yield in future engineering practice. Still, its negative effect on stress adaptability to transgenic plants should also be considered.

Dynamic distress calls: volatile info chemicals induce and regulate defense responses during herbivory

Plants are continuously threatened by a plethora of biotic stresses caused by microbes, pathogens, and pests, which often act as the major constraint in crop productivity. To overcome such attacks, plants have evolved with an array of constitutive and induced defense mechanisms- morphological, biochemical, and molecular. Volatile organic compounds (VOCs) are a class of specialized metabolites that are naturally emitted by plants and play an important role in plant communication and signaling. During herbivory and mechanical damage, plants also emit an exclusive blend of volatiles often referred to as herbivore-induced plant volatiles (HIPVs). The composition of this unique aroma bouquet is dependent upon the plant species, developmental stage, environment, and herbivore species. HIPVs emitted from infested and non-infested plant parts can prime plant defense responses by various mechanisms such as redox, systemic and jasmonate signaling, activation of mitogen-activated protein (MAP) kinases, and transcription factors; mediate histone modifications; and can also modulate the interactions with natural enemies via direct and indirect mechanisms. These specific volatile cues mediate allelopathic interactions leading to altered transcription of defense-related genes, viz., proteinase inhibitors, amylase inhibitors in neighboring plants, and enhanced levels of defense-related secondary metabolites like terpenoids and phenolic compounds. These factors act as deterrents to feeding insects, attract parasitoids, and provoke behavioral changes in plants and their neighboring species. This review presents an overview of the plasticity identified in HIPVs and their role as regulators of plant defense in Solanaceous plants. The selective emission of green leaf volatiles (GLVs) including hexanal and its derivatives, terpenes, methyl salicylate, and methyl jasmonate (MeJa) inducing direct and indirect defense responses during an attack from phloem-sucking and leaf-chewing pests is discussed. Furthermore, we also focus on the recent developments in the field of metabolic engineering focused on modulation of the volatile bouquet to improve plant defenses.

Systematic approaches to C-lignin engineering in Medicago truncatula

BACKGROUND

C-lignin is a homopolymer of caffeyl alcohol present in the seed coats of a variety of plant species including vanilla orchid, various cacti, and the ornamental plant Cleome hassleriana. Because of its unique chemical and physical properties, there is considerable interest in engineering C-lignin into the cell walls of bioenergy crops as a high-value co-product of bioprocessing. We have used information from a transcriptomic analysis of developing C. hassleriana seed coats to suggest strategies for engineering C-lignin in a heterologous system, using hairy roots of the model legume Medicago truncatula.

RESULTS

We systematically tested strategies for C-lignin engineering using a combination of gene overexpression and RNAi-mediated knockdown in the caffeic acid/5-hydroxy coniferaldehyde 3/5-O-methyltransferase (comt) mutant background, monitoring the outcomes by analysis of lignin composition and profiling of monolignol pathway metabolites. In all cases, C-lignin accumulation required strong down-regulation of caffeoyl CoA 3-O-methyltransferase (CCoAOMT) paired with loss of function of COMT. Overexpression of the Selaginella moellendorffii ferulate 5-hydroxylase (SmF5H) gene in comt mutant hairy roots resulted in lines that unexpectedly accumulated high levels of S-lignin.

CONCLUSION

C-Lignin accumulation of up to 15% of total lignin in lines with the greatest reduction in CCoAOMT expression required the strong down-regulation of both COMT and CCoAOMT, but did not require expression of a heterologous laccase, cinnamyl alcohol dehydrogenase (CAD) or cinnamoyl CoA reductase (CCR) with preference for 3,4-dihydroxy-substituted substrates in M. truncatula hairy roots. Cell wall fractionation studies suggested that the engineered C-units are not present in a heteropolymer with the bulk of the G-lignin.

Auxin inhibits lignin and cellulose biosynthesis in stone cells of pear fruit via the PbrARF13-PbrNSC-PbrMYB132 transcriptional regulatory cascade

Stone cells are often present in pear fruit, and they can seriously affect the fruit quality when present in large numbers. The plant growth regulator NAA, a synthetic auxin, is known to play an active role in fruit development regulation. However, the genetic mechanisms of NAA regulation of stone cell formation are still unclear. Here, we demonstrated that exogenous application of 200 μM NAA reduced stone cell content and also significantly decreased the expression level of PbrNSC encoding a transcriptional regulator. PbrNSC was shown to bind to an auxin response factor, PbrARF13. Overexpression of PbrARF13 decreased stone cell content in pear fruit and secondary cell wall (SCW) thickness in transgenic Arabidopsis plants. In contrast, knocking down PbrARF13 expression using virus-induced gene silencing had the opposite effect. PbrARF13 was subsequently shown to inhibit PbrNSC expression by directly binding to its promoter, and further to reduce stone cell content. Furthermore, PbrNSC was identified as a positive regulator of PbrMYB132 through analyses of co-expression network of stone cell formation-related genes. PbrMYB132 activated the expression of gene encoding cellulose synthase (PbrCESA4b/7a/8a) and lignin laccase (PbrLAC5) binding to their promotors. As expected, overexpression or knockdown of PbrMYB132 increased or decreased stone cell content in pear fruit and SCW thickness in Arabidopsis transgenic plants. In conclusion, our study shows that the 'PbrARF13-PbrNSC-PbrMYB132' regulatory cascade mediates the biosynthesis of lignin and cellulose in stone cells of pear fruit in response to auxin signals and also provides new insights into plant SCW formation.

Genome-wide analysis of the Populus trichocarpa laccase gene family and functional identification of PtrLAC23

INTRODUCTION

Biofuel is a kind of sustainable, renewable and environment friendly energy. Lignocellulose from the stems of woody plants is the main raw material for "second generation biofuels". Lignin content limits fermentation yield and is therefore a major obstacle in biofuel production. Plant laccase plays an important role in the final step of lignin formation, which provides a new strategy for us to obtain ideal biofuels by regulating the expression of laccase genes to directly gain the desired lignin content or change the composition of lignin.

METHODS

Multiple sequence alignment and phylogenetic analysis were used to classify PtrLAC genes; sequence features of PtrLACs were revealed by gene structure and motif composition analysis; gene duplication, interspecific collinearity and Ka/Ks analysis were conducted to identify ancient PtrLACs; expression levels of PtrLAC genes were measured by RNA-Seq data and qRT-PCR; domain analysis combine with cis-acting elements prediction together showed the potential function of PtrLACs. Furthermore, Alphafold2 was used to simulate laccase 3D structures, proLAC23::LAC23-eGFP transgenic Populus stem transects were applied to fluorescence observation.

RESULTS

A comprehensive analysis of the P. trichocarpa laccase gene (PtLAC) family was performed. Some ancient PtrLAC genes such as PtrLAC25, PtrLAC19 and PtrLAC41 were identified. Gene structure and distribution of conserved motifs clearly showed sequence characteristics of each PtrLAC. Combining published RNA-Seq data and qRT-PCR analysis, we revealed the expression pattern of PtrLAC gene family. Prediction results of cis-acting elements show that PtrLAC gene regulation was closely related to light. Through above analyses, we selected 5 laccases and used Alphafold2 to simulate protein 3D structures, results showed that PtrLAC23 may be closely related to the lignification. Fluorescence observation of proLAC23::LAC23-eGFP transgenic Populus stem transects and qRT-PCR results confirmed our hypothesis again.

DISCUSSION

In this study, we fully analyzed the Populus trichocarpa laccase gene family and identified key laccase genes related to lignification. These findings not only provide new insights into the characteristics and functions of Populus laccase, but also give a new understanding of the broad prospects of plant laccase in lignocellulosic biofuel production.

Genome-wide identification and characterization of LcCCR13 reveals its potential role in lignin biosynthesis in Liriodendron chinense

Introduction

Wood formation is closely related to lignin biosynthesis. Cinnamoyl-CoA reductase (CCR) catalyzes the conversion of cinnamoyl-CoA to cinnamaldehydes, which is the initiation of the lignin biosynthesis pathway and a crucial point in the manipulation of associated traits. Liriodendron chinense is an economically significant timber tree. Nevertheless, the underlying mechanism of wood formation in it remains unknown; even the number of LcCCR family members in this species is unclear.

Materials and Results

This study aimed to perform a genome-wide identification of genes(s) involved in lignin biosynthesis in L. chinense via RT-qPCR assays and functional verification. Altogether, 13 LcCCR genes were identified that were divided into four major groups based on structural and phylogenetic features. The gene structures and motif compositions were strongly conserved between members of the same groups. Subsequently, the expression patterns analysis based on RNA-seq data indicated that LcCCR5/7/10/12/13 had high expression in the developing xylem at the stem (DXS). Furthermore, the RT-qPCR assays showed that LcCCR13 had the highest expression in the stem as compared to other tissues. Moreover, the overexpression of the LcCCR13 in transgenic tobacco plants caused an improvement in the CCR activity and lignin content, indicating that it plays a key role in lignin biosynthesis in the stems.

Discussion

Our research lays a foundation for deeper investigation of the lignin synthesis and uncovers the genetic basis of wood formation in L. chinense.

A Joint Transcriptomic and Metabolomic Analysis Reveals the Regulation of Shading on Lignin Biosynthesis in Asparagus

Asparagus belongs to the Liliaceae family and has important economic and pharmacological value. Lignin plays a crucial role in cell wall structural integrity, stem strength, water transport, mechanical support and plant resistance to pathogens. In this study, various biological methods were used to study the mechanism of shading on the asparagus lignin accumulation pathway. The physiological results showed that shading significantly reduced stem diameter and cell wall lignin content. Microstructure observation showed that shading reduced the number of vascular bundles and xylem area, resulting in decreased lignin content, and thus reducing the lignification of asparagus. Cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol are crucial intermediate metabolites in the process of lignin synthesis. Metabolomic profiling showed that shading significantly reduced the contents of cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol. Transcriptome profiling identified 37 differentially expressed genes related to lignin, including PAL, C4H, 4CL, CAD, CCR, POD, CCoAOMT, and F5H related enzyme activity regulation genes. The expression levels of POD, CCoAOMT, and CCR genes were significantly decreased under shading treatment, while the expression levels of CAD and F5H genes exhibited no significant difference with increased shading. The downregulation of POD, CCoAOMT genes and the decrease in CCR gene expression levels inhibited the activities of the corresponding enzymes under shading treatment, resulting in decreased downstream content of caffeic acid, ferulic acid, sinaperol, chlorogenic acid and coniferin. A significant decrease in upstream cinnamic acid content was observed with shading, which also led to decreased downstream metabolites and reduced asparagus lignin content. In this study, transcriptomic and metabolomic analysis revealed the key regulatory genes and metabolites of asparagus lignin under shading treatment. This study provides a reference for further understanding the mechanism of lignin biosynthesis and the interaction of related genes.

Biochemical Aspects of the Spiral Grain Formation in Scots Pine (Pinus Sylvestris L.) Wood. Some Differences and Similarities with Biochemical Indicators of Abnormal Xylogenesis in Karelian Birch (Betula Pendula Roth Var. Carelica (Mercl.) Hämet-Ahti)

BACKGROUND

AOS enzymes can be biochemical indicators of abnormal xylogenesis in Scots pine, and this mechanism has similar features with the metabolic base of abnormal xylogenesis in Karelian birch.

OBJECTIVE

AOS enzymes' activity in 150-300-year-old Pinus sylvestris L. wood with straight-- grained wood and right-twisted spiral-grained wood, expressed in varying degrees (5-20 angle), grew in three sample plots in lingonberry and blueberry pine forest stands of different ages (100-300 years) in the middle taiga subzone in the Republic of Karelia.

METHODS

Plant tissues were ground in liquid nitrogen in a uniform mass and homogenized at 4°C in the buffer containing 50 mM HEPES (pH 7.5), 1 mM EDTA, 1 mM EGTA, 3 mM DTT, 5 mM MgCl2 and 0.5 mM PMSF. After 20 min extraction, the homogenate was centrifuged at 10000 g for 20 min (MPW-351R, Poland). The sediment was washed in the buffer thrice. The pooled supernatant and sediment were dialyzed at 4°C for 18-20 h against a tenfold diluted homogenization buffer. The enzymes' activity was determined spectrophotometrically (Spectrophotometer SF-2000, OKB Spectr, Russia). Proteins in the extracts were quantified by the method of Bradford.

RESULTS

The study showed that the activity of SS, ApInv, CAT, POD and PPO in xylem and PPO in phloem were biochemical indicators for abnormal wood of P. sylvestris. We noticed an increase in sucrose metabolism in the apoplast and the activity of POD and PPO under spiral-grain wood formation like under figured wood formation earlier. We assume that the alternative pathway of sucrose metabolism (an indicator of abnormal xylogenesis in B. pendula var. carelica plants) that lead to restructuring of AOS enzymes have the same biochemical regularities in the spiral-grain wood formation in P. sylvestris.

CONCLUSION

The study showed that the differences in the AOS enzyme's activity in P. sylvestris during the formation of straight-grained and spiral-grained wood were revealed for the first time. The increased CAT, POD and PPO activities in xylem with a decrease in SS and an increase in Ap- Inv during spiral-grained wood formation can be biochemical markers of these structural anomalies. Metabolic regularities found in the AOS enzyme complex during spiral-grained wood formation do not contradict those found earlier during figured wood formation in B. pendula var. carelica. The identified patterns can form the base for diagnostics of P. sylvestris wood quality in forest seed plantations and in their natural growth, which is necessary both for fundamental science and in various industry areas while high-quality material harvesting.

Microbial lignin valorization through depolymerization to aromatics conversion

Lignin is the most abundant source of renewable aromatic biopolymers and its valorization presents significant value for biorefinery sustainability, which promotes the utilization of renewable resources. However, it is challenging to fully convert the structurally complex, heterogeneous, and recalcitrant lignin into high-value products. The in-depth research on the lignin degradation mechanism, microbial metabolic pathways, and rational design of new systems using synthetic biology have significantly accelerated the development of lignin valorization. This review summarizes the key enzymes involved in lignin depolymerization, the mechanisms of microbial lignin conversion, and the lignin valorization application with integrated systems and synthetic biology. Current challenges and future strategies to further study lignin biodegradation and the trends of lignin valorization are also discussed.

Getting to the root of Ralstonia invasion

Plant diseases caused by soilborne pathogens are a major limiting factor in crop production. Bacterial wilt disease, caused by soilborne bacteria in the Ralstonia solanacearum Species Complex (Ralstonia), results in significant crop loss throughout the world. Ralstonia invades root systems and colonizes plant xylem, changing plant physiology and ultimately causing plant wilting in susceptible varieties. Elucidating how Ralstonia invades and colonizes plants is central to developing strategies for crop protection. Here we review Ralstonia pathogenesis from root detection and attachment, early root colonization, xylem invasion and subsequent wilting. We focus primarily on studies in tomato from the last 5-10 years. Recent work has identified elegant mechanisms Ralstonia uses to adapt to the plant xylem, and has discovered new genes that function in Ralstonia fitness in planta. A picture is emerging of an amazingly versatile pathogen that uses multiple strategies to make its surrounding environment more hospitable and can adapt to new environments.

De novo transcriptome profiling unveils the regulation of phenylpropanoid biosynthesis in unripe Piper nigrum berries

BACKGROUND

Black pepper (Piper nigrum L.) is rich in bioactive compounds that make it an imperative constituent in traditional medicines. Although the unripe fruits have long been used in different Ayurvedic formulations, the mechanism of gene regulation resulting in the production of the bioactive compounds in black pepper is not much investigated. Exploring the regulatory factors favouring the production of bioactive compounds ultimately help to accumulate the medicinally important content of black pepper. The factors that enhance the biosynthesis of these compounds could be potential candidates for metabolic engineering strategies to obtain a high level production of significant biomolecules.

RESULTS

Being a non-model plant, de novo sequencing technology was used to unravel comprehensive information about the genes and transcription factors that are expressed in mature unripe green berries of P. nigrum from which commercially available black pepper is prepared. In this study, the key gene regulations involved in the synthesis of bioactive principles in black pepper was brought out with a focus on the highly expressed phenylpropanoid pathway genes. Quantitative real-time PCR analysis of critical genes and transcription factors in the different developmental stages from bud to the mature green berries provides important information useful for choosing the developmental stage that would be best for the production of a particular bioactive compound. Comparison with a previous study has also been included to understand the relative position of the results obtained from this study.

CONCLUSIONS

The current study uncovered significant information regarding the gene expression and regulation responsible for the bioactivity of black pepper. The key transcription factors and enzymes analyzed in this study are promising targets for achieving a high level production of significant biomolecules through metabolic engineering.

Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination

Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.

Engineering Curcumin Biosynthesis in Poplar Affects Lignification and Biomass Yield

Lignocellulosic biomass is recalcitrant toward deconstruction into simple sugars mainly due to the presence of lignin. By engineering plants to partially replace traditional lignin monomers with alternative ones, lignin degradability and extractability can be enhanced. Previously, the alternative monomer curcumin has been successfully produced and incorporated into lignified cell walls of Arabidopsis by the heterologous expression of DIKETIDE-CoA SYNTHASE (DCS) and CURCUMIN SYNTHASE2 (CURS2). The resulting transgenic plants did not suffer from yield penalties and had an increased saccharification yield after alkaline pretreatment. Here, we translated this strategy into the bio-energy crop poplar. Via the heterologous expression of DCS and CURS2 under the control of the secondary cell wall CELLULOSE SYNTHASE A8-B promoter (ProCesA8-B), curcumin was also produced and incorporated into the lignified cell walls of poplar. ProCesA8-B:DCS_CURS2 transgenic poplars, however, suffered from shoot-tip necrosis and yield penalties. Compared to that of the wild-type (WT), the wood of transgenic poplars had 21% less cellulose, 28% more matrix polysaccharides, 23% more lignin and a significantly altered lignin composition. More specifically, ProCesA8-B:DCS_CURS2 lignin had a reduced syringyl/guaiacyl unit (S/G) ratio, an increased frequency of p-hydroxyphenyl (H) units, a decreased frequency of p-hydroxybenzoates and a higher fraction of phenylcoumaran units. Without, or with alkaline or hot water pretreatment, the saccharification efficiency of the transgenic lines was equal to that of the WT. These differences in (growth) phenotype illustrate that translational research in crops is essential to assess the value of an engineering strategy for applications. Further fine-tuning of this research strategy (e.g., by using more specific promoters or by translating this strategy to other crops such as maize) might lead to transgenic bio-energy crops with cell walls more amenable to deconstruction without settling in yield.

Deciphering the linkage type and structural characteristics of the p-hydroxyphenyl unit in Pinus massoniana Lamb compressed wood lignin

To reveal the existence of p-hydroxyphenyl (H) units in compressed wood lignin, four different milled wood lignins were extracted using Pinus massoniana Lamb compressed wood, Pinus massoniana Lamb normal wood, and sugarcane bagasse as raw materials. Then, three dehydrogenation polymers (DHPs) were synthesized using coniferyl/p-coumaryl alcohol as raw materials to reveal the interunit linkages of H units. The lignin and DHP samples were systematically characterized by ¹H, ¹³C, 2D HSQC, and ³¹P NMR techniques. Compared with the opposite wood milled wood lignin (OW-MWL) and the normal wood milled wood lignin (NW-MWL), the compressed wood milled wood lignin (CW-MWL) contained a large amount of H units, and the H/G ratio and the p-hydroxyphenyl OH group contents were 0.15 and 1.09 mmol/g, respectively. Through the characterization of CW-MWL and DHPs, it was revealed that p-hydroxyphenyl units mainly coupled with other units by β-O-4, β-β, and β-5 linkages. Compared to the sugarcane bagasse milled wood lignin, it was clearly demonstrated that the H unit rather than p-coumarate ester occurred in CW-MWL. This study comprehensively explored the structural characteristics and linkages of H units in compress wood lignin, and provided useful information for revealing the participation of H units in the construction of lignin macromolecules.

Analysis of the Fruit Quality of Pear (Pyrus spp.) Using Widely Targeted Metabolomics

Pear is a kind of common temperate fruit, whose metabolite composition that contributes to the difference in fruit quality is unclear. This study identified and quantified the metabolites using a widely targeted LC-MS/MS approach in three pear species, including Pyrus bretschneideri (PB), Pyrus usssuriensis (PU) and Pyrus pyrifolia (PP). A total of 493 metabolites were identified, consisting of 68 carbohydrates, 47 organic acids, 50 polyphenols, 21 amino acids, 20 vitamins, etc. The results of PCA and OPLS-DA demonstrated that the metabolite compositions differed distinctly with cultivar variability. Our results also involved some metabolic pathways that may link to the fruit quality based on KEGG pathway analysis, the pathway of phenylalanine metabolism revealed significant differences between PB and PP (p < 0.05). Furthermore, the study selected D-xylose, formononetin, procyanidin A1 and β-nicotinamide mononucleotide as the major differentially expressed metabolites in the three species. The present study can open new avenues for explaining the differences in fruit quality of the major commercial pear cultivars in China.

Effects of season, variety type, and trait on dry matter yield, nutrient composition, and predicted intake and milk yield of whole-plant sorghum forage

Sorghum forage is an important alternative to high-quality forage in regions where climatic and soil conditions are less desirable for corn production for silage and producing comparable nutritive value is challenging. The objective of this experiment was to assess the effects of season (spring vs. summer), sorghum variety type (forage sorghum vs. sorghum-sudangrass), and trait [brown midrib (BMR) vs. non-BMR] on dry matter (DM) yield, nutrient composition, and predicted intake and milk yield of whole-plant sorghum forage grown in Florida from 2008 to 2019. Whole-plant sorghum forage was harvested at a targeted 32% of DM, and each year, spring (April) and summer (July) trials were established. A total of 300 forage sorghum and 137 sorghum-sudangrass hybrids were tested for a total of 437 hybrids, of which 199 hybrids contained the BMR trait and 238 were non-BMR. An interaction between season and sorghum variety type was observed for DM yield. Dry matter yield was greater for the spring season than the summer season, with sorghum-sudangrass outperforming forage sorghum only during the spring season. In addition, BMR hybrids had a lower DM yield than non-BMR hybrids, regardless of season and variety type. An interaction between season and trait was observed for predicted neutral detergent fiber digestibility after 30 h of incubation in rumen fluid (NDFD_30h). Predicted NDFD_30h was greater for BMR sorghum in comparison to non-BMR sorghum, but BMR sorghum had slightly greater predicted NDFD_30h when grown in the spring than summer, whereas no seasonal differences were found for predicted NDFD_30h across non-BMR sorghum. An interaction between season, variety type, and trait was observed for predicted dry matter intake at 45 (DMI₄₅), 55 (DMI₅₅), and 65 (DMI₆₅) kg of milk/d. Predicted DMI₄₅ and DMI₅₅ were greater for spring BMR forage sorghum than for spring and summer non-BMR sorghum-sudangrass and were greater for spring BMR forage sorghum than for summer BMR sorghum-sudangrass. Predicted DMI₆₅ was greater for BMR forage sorghum in comparison to all non-BMR hybrids in the spring. Additionally, spring BMR forage sorghum was greater than summer sorghum-sudangrass regardless of trait. An interaction between season and sorghum variety type was observed for milk yield per megagram of forage. Milk yield per megagram of forage was greatest for spring forage sorghum. Sorghum variety type and trait selection are crucial to minimize differences in forage nutritive value of sorghum forage between seasons and improve the performance of high-producing dairy cows.

Evolution of Physicochemical Properties, Phenolic Acid Accumulation, and Dough-Making Quality of Whole Wheat Flour During Germination Under UV-B Radiation

The effects of ultraviolet-B (UV-B) radiation on the physiological properties, phenolic acid accumulation, and dough-making quality of wheat during germination were investigated. UV-B radiation inhibited the wheat sprout length and reduced the dry matter loss. As phenolic acids were principally present in the kernels' bran, UV-B radiation could promote their accumulation in the interior of germinated wheat (GW). The total phenolic compounds, ascorbic acid, and antioxidant activity were also enhanced significantly during germination with UV-B. UV-B improved the development time, stability time, rheological properties, and viscosity of GW, and inhibited the α-amylase activity, the destruction of the amorphous region of starch particles, and the proteins degradation process during germination, and thus the deterioration of dough-making quality caused by germination was inhibited. Therefore, UV-B radiation could be a potential approach to enhance the nutritional and dough-making quality of germinated whole wheat flour.

Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review

Biodiesel is a renewable fuel that can be produced from a range of organic and renewable feedstock including fresh or vegetable oils, animal fats, and oilseed plants. In recent years, the lignin-based aromatic wastes, such as various aromatic waste polymers from agriculture, or organic dye wastewater from textile industry, have attracted much attention in academia, which can be uniquely selected as a potential renewable feedstock for biodiesel product converted by yeast cell factory technology. This current investigation indicated that the highest percentage of lipid accumulation can be achieved as high as 47.25% by an oleaginous yeast strain, Meyerozyma caribbica SSA1654, isolated from a wood-feeding termite gut system, where its synthetic oil conversion ability can reach up to 0.08 (g/l/h) and the fatty acid composition in yeast cells represents over 95% of total fatty acids that are similar to that of vegetable oils. Clearly, the use of oleaginous yeasts, isolated from wood-feeding termites, for synthesizing lipids from aromatics is a clean, efficient, and competitive path to achieve "a sustainable development" towards biodiesel production. However, the lacking of potent oleaginous yeasts to transform lipids from various aromatics, and an unknown metabolic regulation mechanism presented in the natural oleaginous yeast cells are the fundamental challenge we have to face for a potential cell factory development. Under this scope, this review has proposed a novel concept and approach strategy in utilization of oleaginous yeasts as the cell factory to convert aromatic wastes to lipids as the substrate for biodiesel transformation. Therefore, screening robust oleaginous yeast strain(s) from wood-feeding termite gut system with a set of the desirable specific tolerance characteristics is essential. In addition, to reconstruct a desirable metabolic pathway/network to maximize the lipid transformation and accumulation rate from the aromatic wastes with the applications of various "omics" technologies or a synthetic biology approach, where the work agenda will also include to analyze the genome characteristics, to develop a new base mutation gene editing technology, as well as to clarify the influence of the insertion position of aromatic compounds and other biosynthetic pathways in the industrial chassis genome on the expressional level and genome stability. With these unique designs running with a set of the advanced biotech approaches, a novel metabolic pathway using robust oleaginous yeast developed as a cell factory concept can be potentially constructed, integrated and optimized, suggesting that the hypothesis we proposed in utilizing aromatic wastes as a feedstock towards biodiesel product is technically promising and potentially applicable in the near future.

Lignin as a Bio-Sourced Secondary Template for ZSM-5 Zeolite Synthesis

The aim of this study was to investigate the effect of the addition of lignin as a sacrificial agent in ZSM-5 zeolite synthesis. Peculiar growths of ZSM-5 crystals leading to various textural properties were observed. Hence, the behavior in acid-catalyzed conversion of methanol into hydrocarbons (MTH) shifted from high selectivity toward olefins (>55%) to the sole formation of dimethyl ether (DME). Lignin acted as a bio-sourced secondary template (BSST), impacting the zeolite crystals’ shape and, thus, their physicochemical properties.

Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity

The factors controlling lignin composition remain unclear. Catechyl (C)-lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.

Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes

BACKGROUND

Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss.

METHODS

Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress.

RESULTS

It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.

Utilization of exogenous fibrolytic enzymes in fiber fermentation, degradation, and digestions and characteristics of whole legume faba bean and its plant silage

This article aims to review recent progress and update on utilization of exogenous fibrolytic enzymes in fiber fermentation, degradation, and digestions and nutritive and anti-nutritional characteristics of whole legume faba bean and its silage. The study focused on strategies to improve the utilization and bioavailability of fiber through pre-treating exogenous fibrolytic enzymes. The review includes features of nutrition and anti-nutritional factors and environment impact, forage fiber fermentation, degradation and digestion, legume bean in various diets, use of exogenous enzyme and factor affecting enzyme action in fiber digestion as well as exogenous enzyme response. This review also provides very recent research on effects of fibrolytic enzyme on rumen degradation characteristics of dry matter and fiber of whole plant faba bean silage and effect of exogenous fibrolytic enzyme derived from trichoderma reesei on lactational performance, feeding behavior, rumen fermentation and nutrient digestibility in dairy cows fed whole plant faba bean silage-based diet. This study provides an insight on nutritive and anti-nutritive characteristics of whole legume bean and its plant silage and utilization of exogenous fibrolytic enzymes in fiber fermentation, degradation, and digestions.

Comparative Molecular Mechanisms of Biosynthesis of Naringenin and Related Chalcones in Actinobacteria and Plants: Relevance for the Obtention of Potent Bioactive Metabolites

Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P₄₅₀ monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P₄₅₀ monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described.

Local Variations in Carbohydrates and Matrix Lignin in Mechanically Graded Bamboo Culms

The mechanical performance of bamboo is highly dependent on its structural arrangement and the properties of biomacromolecules within the cell wall. The relationship between carbohydrates topochemistry and gradient micromechanics of multilayered fiber along the diametric direction was visualized by combined microscopic techniques. Along the radius of bamboo culms, the concentration of xylan within the fiber sheath increased, while that of cellulose and lignin decreased gradually. At cellular level, although the consecutive broad layer (Bl) of fiber revealed a relatively uniform cellulose orientation and concentration, the outer Bl with higher lignification level has higher elastic modulus (19.59-20.31 GPa) than that of the inner Bl close to the lumen area (17.07-19.99 GPa). Comparatively, the cell corner displayed the highest lignification level, while its hardness and modulus were lower than that of fiber Bl, indicating the cellulose skeleton is the prerequisite of cell wall mechanics. The obtained cytological information is helpful to understand the origin of the anisotropic mechanical properties of bamboo.

Hypolignification: A Decisive Factor in the Development of Hyperhydricity

One of the characteristics of hyperhydric plants is the reduction of cell wall lignification (hypolignification), but how this is related to the observed abnormalities of hyperhydricity (HH), is still unclear. Lignin is hydrophobic, and we speculate that a reduction in lignin levels leads to more capillary action of the cell wall and consequently to more water in the apoplast. p-coumaric acid is the hydroxyl derivative of cinnamic acid and a precursor for lignin and flavonoids in higher plant. In the present study, we examined the role of lignin in the development of HH in Arabidopsis thaliana by checking the wild-types (Ler and Col-0) and mutants affected in phenylpropanoid biosynthesis, in the gene coding for cinnamate 4-hydroxylase, C4H (ref3-1 and ref3-3). Exogenously applied p-coumaric acid decreased the symptoms of HH in both wild-type and less-lignin mutants. Moreover, the results revealed that exogenously applied p-coumaric acid inhibited root growth and increased the total lignin content in both wild-type and less-lignin mutants. These effects appeared to diminish the symptoms of HH and suggest an important role for lignin in HH.

Effects of harvest intervals and seeding rates on dry matter yield and nutritive value of alfalfa cultivars

Maturation process of alfalfa (Medicago sativa L.) could be prevented by the reduction of lignin content in terms of conventional breeding or transgenic technology. Alfalfa could exhibit higher leaf/stem ratio, with a concern of yield loss. The objective of this study was to compare forage yield and nutritive value of low lignin alfalfa and two reference varieties subjecting to two harvest intervals and three seeding rates. The experimental design was a randomized complete block in a split-split plot arrangement with four replicates, where harvest intervals (28-day and 35-day) were assigned to whole plots, seeding rates were subplots, and varieties were sub-subplots. The weighted mean nutritive value was applied to two production years of 2016 and 2017. Hi-Gest 360 (low lignin alfalfa) provided similar yield potential and increased nutritive value compared to two reference varieties. Over a two-year production period, alfalfa harvested at every 28-day interval provided more economic returns than those at 35-day interval. For the seeding year and first production year, five cuts made by the 28-day interval produced more yield than four cuts by the 35-day interval. Due to limited rainfall in May 2017, a sharp drop of the first cutting overturned the advantage of the five-cut system. Shorter intervals between harvests generally increased crude protein (CP) concentrations. The differences of relative feed value (RFV) between two harvest intervals tended to be great during the first and second cuttings. Overall, harvest interval had a large effect on nutritive value and a more significant effect on alfalfa dry matter yield than variety selection. Seeding rate did not affect alfalfa yield and nutritive value.

A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

BACKGROUND

Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.

RESULTS

We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation.

CONCLUSIONS

This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.

Intensification of p-coumaric acid heterologous production using extractive biphasic fermentation

p-coumaric acid (p-CA) can be produced from D-glucose by an engineered S. cerevisiae strain. p-CA has antimicrobial properties and retro-inhibition activity. Moreover, p-CA is a hydrophobic compound, limiting its accumulation in fermentation broth. To overcome these issues all at once, a liquid-liquid extraction in-situ product recovery process using oleyl alcohol as extractant has been implemented in order to continuously extract p-CA from the broth. Media and pH impacts on strain metabolism were assessed, highlighting p-CA decarboxylase endogenous activity. Biphasic fermentations allowed an increase in p-CA respiratory production rates at both pH assessed (13.65 and 9.45 mg L^-1.h^-1 at pH 6 and 4.5, respectively) compared to control ones (10.5 and 7.5 mg L^-1.h^-1 at pH 6 and 4.5, respectively). Biphasic fermentation effects on p-CA decarboxylation were studied showing that continuous removal of p-CA decreased its decarboxylation into 4-vinylphenol at pH 4.5 (57 mg L^-1 in biphasic fermentation vs 173 mg L^-1 in control one).

Isolating key reaction energetics and thermodynamic properties during hardwood model lignin pyrolysis

Computational studies on the pyrolysis of lignin using electronic structure methods have been largely limited to dimeric or trimeric models. In the current work we have modeled a lignin oligomer consisting of 10 syringyl units linked through 9 β-O-4' bonds. A lignin model of this size is potentially more representative of the polymer in angiosperms; therefore, we used this representative model to examine the behavior of hardwood lignin during the initial steps of pyrolysis. Using this oligomer, the present work aims to determine if and how the reaction enthalpies of bond cleavage vary with positions within the chain. To accomplish this, we utilized a composite method using molecular mechanics based conformational sampling and quantum mechanically based density functional theory (DFT) calculations. Our key results show marked differences in bond dissociation enthalpies (BDE) with the position. In addition, we calculated standard thermodynamic properties, including enthalpy of formation, heat capacity, entropy, and Gibbs free energy for a wide range of temperatures from 25 K to 1000 K. The prediction of these thermodynamic properties and the reaction enthalpies will benefit further computational studies and cross-validation with pyrolysis experiments. Overall, the results demonstrate the utility of a better understanding of lignin pyrolysis for its effective valorization.

Cloning, expression analysis and molecular marker development of cinnamyl alcohol dehydrogenase gene in common wheat

In common wheat, stem strength is one of the key factors for lodging resistance, which is influenced by lignin content. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme in the pathway of lignin biosynthesis. Cloning and marker development of the CAD gene could be helpful for lodging resistance breeding. In this study, the full-length genomic DNA sequence of CAD gene in wheat was cloned by using homologous strategy. A marker 5-f2r2 was developed based on CAD sequence and used to genotype 258 wheat lines. Four haplotype combinations of CAD genes were identified in 258 wheat lines. Correction analyses among the CAD gene expression, CAD activity, and stem strength indicated significant positive correlation between CAD gene expression and CAD activity, between wheat CAD activity and wheat stem strength. The haplotype combination B is significantly associated with the lower enzyme activity and weak stem strength, which was supported by the level of CAD gene expression. The CAD activity and stem strength of wheat could be distinguished to some extent using this pair of specific primer 5-f2r2 designed in this study, indicating that the sequence targeted site (STS) marker 5-f2r2 could be used in marker assistant selection (MAS) breeding.

Changes in phenotype and gene expression under lead stress revealed key genetic responses to lead tolerance in Medicago sativa L

Lead (Pb) is a serious heavy metal soil pollutant. It can be absorbed and accumulated by plant roots and impact plant growth. Medicago sativa L. (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Little is known about the mechanism by which alfalfa responds to Pb stress at the molecular level. In this study, three alfalfa genotypes (a lead-resistant type (LR), a lead-sensitive type (LS) and an intermediate type (IN)) with contrasting abilities to resist lead were exposed to different durations of Pb treatment. Next-generation sequencing (NGS)-based RNA-seq technology was employed to characterize the root transcriptomes of three genotypes of alfalfa and identify differentially expressed genes (DEGs) during Pb stress. Genotypes LR and LS displayed different mechanisms of tolerance. In LR, the accumulation of more resistant substances was induced by the upregulation of sucrose synthase, glucan endo-1,3-beta-glucosidase, beta-amylase 3, probable trehalose-phosphate phosphatase J, 6-phosphofructo-2-kinase delta-1-pyrroline-5-carboxylate synthase (P5CS) and δ-ornithine aminotransferase (δ-OAT). In addition, flavin monooxygenase (YUCCA), 4-coumarate:CoA ligase-like protein (4CL), cinnamoyl-CoA reductase-like protein (CCR), ferulate 5-hydroxylase (F5H) and caffeic acid O-methyltransferase (COMT) were upregulated, leading to root development in a short time under Pb stress. Further study of the expression levels of metal transport-related genes, such as NRAMP (metal transporter), MATE (multidrug and toxin extrusion), HIPPs (heavy metal-associated isoprenylated plant proteins), MTP (metal tolerance protein), and ABC transporter, suggested that these genes were differentially expressed after lead treatment in the three alfalfa genotypes. Our research provides useful information for further studies on the molecular mechanism of Pb resistance in Medicago sativa L.

Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing

The aim of this study was to examine the regulation of transcriptomics and proteomics related to the yellowing of fresh-cut yams after storage. The comparison of yellow fresh-cut yam (YFY) vs. white fresh-cut yam (control) revealed 6894 upregulated and 6800 downregulated differentially expressed genes along with 1277 upregulated and 677 downregulated differentially expressed proteins. The results showed that the total carotenoids, flavonoids, and bisdemethoxycurcumin in YFY were higher than in the control due to the significant up-regulation of critical genes in the carotenoid biosynthesis pathway, flavonoid biosynthesis pathway, and stilbenoid, diarylheptanoid, and gingerol biosynthesis pathway. In addition, the tricarboxylic acid cycle and phenylpropanoid biosynthesis were both enhanced in YFY compared to the control, providing energy and precursors for the formation of yellow pigments. The results suggest that the synthesis of yellow pigments is regulated by critical genes, which might explain the yellowing of fresh-cut yam after storage.

Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon

BACKGROUND

Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called "esters" pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the "reverse" direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass Brachypodium distachyon has two HCT genes, but lacks a classical CSE gene. This study was therefore conducted to evaluate the utility of HCT as a target for lignin modification in a species with an "incomplete" shikimate shunt.

RESULTS

The kinetic properties of recombinant B. distachyon HCTs were compared with those from Arabidopsis thaliana, Medicago truncatula, and Panicum virgatum (switchgrass) for both the forward and reverse reactions. Along with two M. truncatula HCTs, B. distachyon HCT2 had the least kinetically unfavorable reverse HCT reaction, and this enzyme is induced when HCT1 is down-regulated. Down regulation of B. distachyon HCT1, or co-down-regulation of HCT1 and HCT2, by RNA interference led to reduced lignin levels, with only modest changes in lignin composition and molecular weight.

CONCLUSIONS

Down-regulation of HCT1, or co-down-regulation of both HCT genes, in B. distachyon results in less extensive changes in lignin content/composition and cell wall structure than observed following HCT down-regulation in dicots, with little negative impact on biomass yield. Nevertheless, HCT down-regulation leads to significant improvements in biomass saccharification efficiency, making this gene a preferred target for biotechnological improvement of grasses for bioprocessing.

The Role of Polyphenols in Abiotic Stress Response: The Influence of Molecular Structure

Abiotic stressors such as extreme temperatures, drought, flood, light, salt, and heavy metals alter biological diversity and crop production worldwide. Therefore, it is important to know the mechanisms by which plants cope with stress conditions. Polyphenols, which are the largest group of plant-specialized metabolites, are generally recognized as molecules involved in stress protection in plants. This diverse group of metabolites contains various structures, from simple forms consisting of one aromatic ring to more complex ones consisting of large number of polymerized molecules. Consequently, all these molecules, depending on their structure, may show different roles in plant growth, development, and stress protection. In the present review, we aimed to summarize data on how different polyphenol structures influence their biological activity and their roles in abiotic stress responses. We focused our review on phenolic acids, flavonoids, stilbenoids, and lignans.

Nitrogen Supply Alters Rice Defense Against the Striped Stem Borer Chilo suppressalis

Plant nutrition status is closely associated with plant defense against insect herbivores. However, the way nitrogen supply regulates rice anti-herbivore is not clear. This study investigated the effects of low (LN, 0.3 mM) and high (HN, 3 mM) nitrate levels on rice resistance against the striped stem borer Chilo suppressalis (SSB), one of the major destructive rice pests. Seven-day-old rice seedlings were cultured with different nitrate levels for 30 days and then inoculated with third instars of SSB. LN significantly enhanced rice anti-herbivore defense and lowered the total nitrogen content in the plants, but increased the content of free amino acids after SSB infestation. Additionally, LN significantly increased the accumulation of phenolic acids and flavonoids, especially lignin, resulting in enhanced constitutive defense in SSB-infested plants. SSB feeding led to a rapid accumulation of secondary metabolites. HN application led to the accumulation of metabolites derived from cinnamic acid, p-coumaric acid, p-coumaric CoA, feruloyl CoA, and apigenin, while LN led to the accumulation of metabolites derived from 3-dehydroquinic acid, phenylalanine, acetyl CoA, and aspartic acid. Collectively, our finding suggests that nitrogen deficiency enhances rice anti-herbivore defense via constitutive defense by the accumulation of phenolic acids and flavonoids.

Osmotic Stress Leads to Significant Changes in Rice Root Metabolic Profiles between Tolerant and Sensitive Genotypes

To breed osmotic stress-tolerant rice, the mechanisms involved in maintaining root growth under osmotic stress is important to elucidate. In this study, two rice (Oryza sativa L.) cultivars, IR 58 (stress-tolerant cultivar) and Basilanon (stress-sensitive cultivar), were used. After 1, 3, and 7 days of -0.42 MPa osmotic stress treatment induced by polyethylene glycol (PEG) 6000, root metabolomes were analyzed, yielding 276 detected compounds. Among 276 metabolites, 102 metabolites increased with the duration of the stress treatment in IR 58 roots, and only nine metabolites decreased. In contrast, 51 metabolites increased, and 45 metabolites decreased in Basilanon roots. Principal component analysis (PCA) scores clearly indicated differences between the cultivars and the treatments. Pathway analysis showed that the metabolites exhibiting stress-induced increases in IR 58 were those involved in sugar metabolism (such as sucrose 6'-phosphate, glucose 1-phosphate), polyamine and phenylpropanoid metabolisms (such as spermine, spermidine, gamma-aminobutyric acid (GABA)), and glutathione metabolism (such as glutathione, cysteine, cadaverine). IR 58 roots showed an increase in the most proteinogenic amino acids such as proline, serine, glutamine and asparagine. It was also maintained or increased the tricarboxylic acid (TCA) cycle intermediates (citric acid, cis-Aconitic acid, isocitric acid, fumaric acid, malic acid) under osmotic stress compared with that under control. Therefore, IR 58 actively synthesized various metabolites, and the increase in these metabolites contributed to the maintenance of important biological functions such as energy production and antioxidant defense to promote root development under osmotic stress.