Regulation of Phenylpropanoid Metabolism in Relation to Lignin Biosynthesis in Plants

Climate-responsive DNA methylation is involved in the biosynthesis of lignin in birch

Lignin is one of the most important secondary metabolites and essential to the formation of cell walls. Changes in lignin biosynthesis have been reported to be associated with environmental variations and can influence plant fitness and their adaptation to abiotic stresses. However, the molecular mechanisms underlying this association remain unclear. In this study, we evaluated the relations between the lignin biosynthesis and environmental factors and explored the role of epigenetic modification (DNA methylation) in contributing to these relations if any in natural birch. Significantly negative correlations were observed between the lignin content and temperature ranges. Analyzing the transcriptomes of birches in two habitats with different temperature ranges showed that the expressions of genes and transcription factors (TFs) involving lignin biosynthesis were significantly reduced at higher temperature ranges. Whole-genome bisulfite sequencing revealed that promoter DNA methylation of two NAC-domain TFs, BpNST1/2 and BpSND1, may be involved in the inhibition of these gene expressions, and thereby reduced the content of lignin. Based on these results we proposed a DNA methylation-mediated lignin biosynthesis model which responds to environmental factors. Overall, this study suggests the possibility of environmental signals to induce epigenetic variations that result in changes in lignin content, which can aid to develop resilient plants to combat ongoing climate changes or to manipulate secondary metabolite biosynthesis for agricultural, medicinal, or industrial values.

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.

A rice QTL GS3.1 regulates grain size through metabolic-flux distribution between flavonoid and lignin metabolons without affecting stress tolerance

Grain size is a key component trait of grain weight and yield. Numbers of quantitative trait loci (QTLs) have been identified in various bioprocesses, but there is still little known about how metabolism-related QTLs influence grain size and yield. The current study report GS3.1, a QTL that regulates rice grain size via metabolic flux allocation between two branches of phenylpropanoid metabolism. GS3.1 encodes a MATE (multidrug and toxic compounds extrusion) transporter that regulates grain size by directing the transport of p-coumaric acid from the p-coumaric acid biosynthetic metabolon to the flavonoid biosynthetic metabolon. A natural allele of GS3.1 was identified from an African rice with enlarged grains, reduced flavonoid content and increased lignin content in the panicles. Notably, the natural allele of GS3.1 caused no alterations in other tissues and did not affect stress tolerance, revealing an ideal candidate for breeding efforts. This study uncovers insights into the regulation of grain size though metabolic-flux distribution. In this way, it supports a strategy of enhancing crop yield without introducing deleterious side effects on stress tolerance mechanisms.

Redox Status, JA and ET Signaling Pathway Regulating Responses to Botrytis cinerea Infection Between the Resistant Cucumber Genotype and Its Susceptible Mutant

Botrytis cinerea is an important necrotrophic fungal pathogen with a broad host range and the ability to causing great economic losses in cucumber. However, the resistance mechanism against this pathogen in cucumber was not well understood. In this study, the microscopic observation of the spore growth, redox status measurements and transcriptome analysis were carried out after Botrytis cinerea infection in the resistant genotype No.26 and its susceptible mutant 26M. Results revealed shorter hypha, lower rate of spore germination, less acceleration of H₂O₂, O₂ ^-, and lower total glutathione content (GSH+GSSG) in No.26 than that in 26M, which were identified by the staining result of DAB and NBT. Transcriptome data showed that after pathogen infection, a total of 3901 and 789 different expression genes (DEGs) were identified in No.26 and 26M respectively. These DEGs were highly enriched in redox regulation pathway, hormone signaling pathway and plant-pathogen interaction pathway. The glutathione S-transferase genes, putative peroxidase gene, and NADPH oxidase were up-regulated in No.26 whereas these genes changed little in 26M after Botrytis cinerea infection. Jasmonic acid and ethylene biosynthesis and signaling pathways were distinctively activated in No.26 comparing with 26M upon infection. Much more plant defense related genes including mitogen-activated protein kinases, calmodulin, calmodulin-like protein, calcium-dependent protein kinase, and WRKY transcription factor were induced in No.26 than 26M after pathogen infection. Finally, a model was established which elucidated the resistance difference between resistant cucumber genotype and susceptible mutant after B. cinerea infection.

Hexanal Vapor Induced Resistance against Major Postharvest Pathogens of Banana (Musa acuminata L.)

Hexanal, a C-6 aldehyde has been implicated to have antimicrobial properties. Hence, this study was conducted to determine the antifungal activities of hexanal vapor against major postharvest pathogens of banana viz., Colletotrichum gloeosporioides and Lasiodiplodia theobromae. The pathogens were cultured in vitro and exposed to hexanal vapor at 600, 800, 1,000 and 1,200 ppm. Mycelial growth of both fungal pathogens were inhibited completely at 800 ppm and the incidence of anthracnose and stem-end rot diseases reduced by 75.2% and 80.2%, respectively. The activities of peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase and glucanase had transiently increased in hexanal vapor treated banana by 5 to 7 days and declined thereafter. Postharvest treatment of banana with hexanal vapor resulted in phospholipase D inhibition and also resulted in cell wall thickening of the treated fruit, which impeded the penetration of the pathogenic spores. This was further confirmed by scanning electron micrographs. The defense-related protein intermediaries had increased in hexanal vapor treated banana fruit, which suggests induced resistance against C. gloeosporioides and L. theobromae, via., the phenylpropanoid pathway which plays a significant role in hindering the pathogen quiescence. Delayed ripening due to inhibition of phospholipase D enzyme, inhibition of mycelial growth and induced systemic resistance by defense enzymes collectively contributed to the postharvest disease reduction and extended shelf life of fruit.

Gene expression analysis of bud burst process in European hazelnut (Corylus avellana L.) using RNA-Seq

The control of bud burst process depending on temperature is crucial factor in woody perennial plants to survive in unfavorable ecological conditions. Although it has important economic and agronomic values, little information is available on the molecular mechanism of the bud burst process in Corylus avellana. Here for the first time, we conducted a de novo transcriptome-based experiment using eco-dormant leaf bud tissues. Four transcriptome libraries were constructed from the leaf bud tissues and sequenced via Illumina platform. Transcriptome analysis revealed 86,394 unigenes with a mean length of 1189 nt and an N50 of 1916 nt. Among these unigenes, 63,854 (73.78%) of them were annotated by at least one database. De novo assembled transcripts were enriched in phenylpropanoid metabolism, phytohormone biosynthesis and signal transduction pathways. Analyses of phytohormone-associated genes revealed important changes during bud burst, in response to gibberellic acid, auxin, and brassinosteroids. Approximately 2163 putative transcription factors were predicted, of which the largest number of unique transcripts belonged to the MYB transcription factor family. These results contribute to a better understanding of the regulation of bud burst genes in perennial plants.

Evaluating Changes in Cell-Wall Components Associated with Clubroot Resistance Using Fourier Transform Infrared Spectroscopy and RT-PCR

Clubroot disease is a serious threat to canola production in western Canada and many parts of the world. Rcr1 is a clubroot resistance (CR) gene identified recently and its molecular mechanisms in mediating CR have been studied using several omics approaches. The current study aimed to characterize the biochemical changes in the cell wall of canola roots connecting to key molecular mechanisms of this CR gene identified in prior studies using Fourier transform infrared (FTIR) spectroscopy. The expression of nine genes involved in phenylpropanoid metabolism was also studied using qPCR. Between susceptible (S) and resistance (R) samples, the most notable biochemical changes were related to an increased biosynthesis of lignin and phenolics. These results were supported by the transcription data on higher expression of BrPAL1. The up-regulation of PAL is indicative of an inducible defence response conferred by Rcr1; the activation of this basal defence gene via the phenylpropanoid pathway may contribute to clubroot resistance conferred by Rcr1. The data indicate that several cell-wall components, including lignin and pectin, may play a role in defence responses against clubroot. Principal components analysis of FTIR data separated non-inoculated samples from inoculated samples, but not so much between inoculated S and inoculated R samples. It is also shown that FTIR spectroscopy can be a useful tool in studying plant-pathogen interaction at cellular levels.

Cloning and characterisation of a phenylalanine ammonia-lyase gene from Rhus chinensis

The gene and cDNA sequence encoding PAL from Chinese medicinal plant Rhus chinensis were cloned and analyzed, furthermore the biochemical properties, kinetic parameters, differential expression and key sites were studied. Rhus chinensis is a well-known Chinese medicinal plant. Phenylalanine ammonia-lyase (PAL) is the first enzyme of phenylpropanoid pathway. Several recent studies suggested that PAL also play an important role in plant-aphid interaction. In this study, both the cDNA and the genomic sequence encoding PAL from Rhus chinensis (designated as RcPAL) were cloned and analyzed. The 3,833 bp gene contained a 1,342 bp intron and two extrons. The ORF was 2,124 bp and predicted to encode a 707-amino acid polypeptide. The results of real-time PCR showed that RcPAL expressed in all tested tissues and followed the order: stems > young leaves > petioles > roots > seeds > mature leaves. RcPAL was successfully expressed in E. coli with the pET-28a-RcPAL recombinant vector. The recombinant protein exhibited a high level of PAL activity. Biochemical properties and kinetic parameters of recombinant RcPAL were further studied. The results showed that the optimal temperature and pH for RcPAL activity were 45 °C and 9.0, and the K m and K cat values were 7.90 mM and 52.31 s(-1), respectively. The active sites and substrate selectivity site were also investigated with site-directed mutagenesis methods, suggesting that Phe(126) is responsible for the substrate selectivity. To our knowledge, this was the first full-length PAL gene cloned and characterized from the family Anacardiaceae so far.

Molecular and analysis of a phenylalanine ammonia-lyase gene (LrPAL2) from Lycoris radiata

Phenylalanine ammonia-lyase (PAL), the first enzyme of phenylpropanoid biosynthesis, participates in the biosynthesis of flavonoids, lignins, stilbenes and many other compounds. In this study, we cloned a 2,326 bp full-length PAL2 gene from Lycoris radiata by using degenerate oligonucleotide primer PCR (DOP-PCR) and the rapid amplification of cDNA ends method. The cDNA contains a 2,124 bp coding region encoding 707 amino acids. The LrPAL2 shares about 77.0 % nucleic acid identity and 83 % amino acid identity with LrPAL1. Furthermore, genome sequence analysis demonstrated that LrPAL2 gene contains one intron and two exons. The 5' flanking sequence of LrPAL2 was also cloned by self-formed adaptor PCR (SEFA-PCR), and a group of putative cis-acting elements such as TATA box, CAAT box, G box, TC-rich repeats, CGTCA motif and TCA-element were identified. The LrPAL2 was detected in all tissues examined, with high abundance in bulbs at leaf sprouting stage and in petals at blooming stage. Besides, LrPAL2 drastically responded to MJ, SNP and UV, moderately responded to GA and SA, and a little increased under wounding. Comparison of LrPAL2 expression and LrPAL1 expression demonstrated that LrPAL2 can be more significantly induced than LrPAL1 under the above treatments, and LrPAL2 transcripts accumulated prominently at blooming stage, especially in petals, while LrPAL1 transcripts did not accumulated significantly at blooming stage. All these results suggested that LrPAL2 might play distinct roles in different branches of the phenylpropanoid pathway.

Molecular cloning and characterization of phenylalanine ammonia-lyase and cinnamate 4-hydroxylase in the phenylpropanoid biosynthesis pathway in garlic (Allium sativum)

The cDNAs encoding phenylalanine ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H) were cloned from garlic (Allium sativum) using reverse transcription-polymerase chain reaction (RT-PCR) with degenerate primers and 5' and 3' rapid amplification of cDNA ends (RACE) PCR. Amino acid sequence alignments showed that AsPAL and AsC4H have more than 70% amino acid identity with their homologues in other plants. The expression of AsPAL and AsC4H transcripts was highest in the roots but surprisingly low in the bulbils, where phenylpropanoid compounds are most concentrated. These results suggest that some phenylpropanoids are synthesized in the roots and subsequently transported to the bulbils of A. sativum .

Molecular cloning and characterization of a phenylalanine ammonia-lyase gene (LrPAL) from Lycoris radiata

LrPAL is a novel full-length cDNA isolated from Lycoris radiata by degenerate oligonucleotide primer PCR (DOP-PCR), 3'- and 5'-RACE approaches, harbours an open reading frame (ORF) encoding a 708 amino acid product. Sequence alignment showed that the deduced amino acid sequence of LrPAL shared more than 80% identity with other PAL sequences reported in Arabidopsis thaliana and other plants. RT-PCR revealed that LrPAL transcripts were higher in bud flowers and wilting flowers (5 days after blooming) than in blooming flowers. The transcript levels of LrPAL in leaves were significantly induced by methyl jasmonate (MJ) and nitric oxide (NO), and salicylic acid (SA). Similarly, HPLC analysis showed that galantamine (GAL) content was also higher in bud flowers and wilting flowers than in blooming flowers. The GAL content in leaves was significantly induced by MJ and NO, and inhibited by SA. This study enables us to further elucidate the role of LrPAL in the biosynthesis of GAL in Lycoris radiata at a molecular level.

Molecular cloning, expression and characterization of a phenylalanine ammonia-lyase gene (SmPAL1) from Salvia miltiorrhiza

Phenylalanine ammonia-lyase (PAL) is one of the branch point enzymes between primary and secondary metabolism. It plays an important role during plant development and defense. A PAL gene designated as SmPAL1 was cloned from Salvia miltiorrhiza using genome walking technology. The full-length SmPAL1 was 2,827 bp in size and consisted of an intron and two extrons encoding a 711-amino-acid polypeptide. Sequence alignment revealed that SmPAL1 shared more than 80% identity with the PAL sequences reported in Arabidopsis thaliana and other plants. The 5' flanking sequence of SmPAL1 was also cloned, and a group of putative cis-acting elements such as TATA box, CAAT box, G box and TC-rich repeats were identified. Transcription pattern analysis indicated that SmPAL1 expressed in all tissues examined, but more highly in leaf. Besides, expression of SmPAL1 was found to be induced by various treatments including ABA, wounding, and dehydration. To further confirm its function, SmPAL1 was expressed in Escherichia coli strain M15 with pQE-30 vector. The recombinant protein exhibited high PAL activity and could catalyze the conversion of L: -Phe to trans-cinnamic acid. This study will enable us to further understand the role SmPAL1 plays in the synthesis of active pharmaceutical compounds in S. miltiorrhiza at molecular level.

Molecular cloning of two genes encoding cinnamate 4-hydroxylase (C4H) from oilseed rape (Brassica napus)

Cinnamate 4-hydroxylase (C4H) is a key enzyme of phenylpropanoid pathway, which synthesizes numerous secondary metabolites to participate in development and adaption. Two C4H isoforms, the 2192-bp BnC4H-1 and 2108-bp BnC4H-2, were cloned from oilseed rape (Brassica napus). They both have two introns and a 1518-bp open reading frame encoding a 505-amino-acid polypeptide. BnC4H-1 is 57.73 kDa with an isoelectric point of 9.11, while 57.75 kDa and 9.13 for BnC4H-2. They share only 80.6% identities on nucleotide level but 96.6% identities and 98.4% positives on protein level. Showing highest homologies to Arabidopsis thaliana C4H, they possess a conserved p450 domain and all P450-featured motifs, and are identical to typical C4Hs at substrate-recognition sites and active site residues. They are most probably associated with endoplasmic reticulum by one or both of the N- and C-terminal transmembrane helices. Phosphorylation may be a necessary post-translational modification. Their secondary structures are dominated by alpha helices and random coils. Most helices locate in the central region, while extended strands mainly distribute before and after this region. Southern blot indicated about 9 or more C4H paralogs in B. napus. In hypocotyl, cotyledon, stem, flower, bud, young- and middle-stage seed, they are co-dominantly expressed. In root and old seed, BnC4H-2 is dominant over BnC4H-1, with a reverse trend in leaf and pericarp. Paralogous C4H numbers in Brassicaceae genomes and possible roles of conserved motifs in 5' UTR and the 2nd intron are discussed.

Modification of phenolic metabolism in soybean hairy roots through down regulation of chalcone synthase or isoflavone synthase

Soybean hairy roots, transformed with the soybean chalcone synthase (CHS6) or isoflavone synthase (IFS2) genes, with dramatically decreased capacity to synthesize isoflavones were produced to determine what effects these changes would have on susceptibility to a fungal pathogen. The isoflavone and coumestrol concentrations were decreased by about 90% in most lines apparently due to gene silencing. The IFS2 transformed lines had very low IFS enzyme activity in microsomal fractions as measured by the conversion of naringenin to genistein. The CHS6 lines with decreased isoflavone concentrations had 5 to 20-fold lower CHS enzyme activities than the appropriate controls. Both IFS2 and CHS transformed lines accumulated higher concentrations of both soluble and cell wall bound phenolic acids compared to controls with higher levels found in the CHS6 lines indicating alterations in the lignin biosynthetic branch of the pathway. Induction of the soybean phytoalexin glyceollin, of which the precursor is the isoflavone daidzein, by the fungal pathogen Fusarium solani f. sp. glycines (FSG) that causes soybean sudden death syndrome (SDS) showed that the low isoflavone transformed lines did not accumulate glyceollin while the control lines did. The (iso)liquritigenin content increased upon FSG induction in the IFS2 transformed roots indicating that the pathway reactions before this point can control isoflavonoid synthesis. The lowest fungal growth rate on hairy roots was found on the FSG partially resistant control roots followed by the SDS sensitive control roots and the low isoflavone transformants. The results indicate the importance of phytoalexin synthesis in root resistance to the pathogen.

Overlapping expression of cytosolic glutamine synthetase and phenylalanine ammonia-lyase in immature leaf blades of rice

In order to estimate whether cytosolic glutamine synthetase (GS1; EC 6.3.1.2) is partly coupled to the reaction of phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) in developing organs of rice (Oryza sativa L.), we compared the expression pattern of transcripts and proteins for GS1 and PAL in the tissue sections from leaf blades at various stages of development. In immature vascular bundles of unexpanded leaf blades, GS1 mRNA was mainly detected in xylem parenchyma cells, mestome-sheath cells, and sclerenchyma cells. PAL transcripts were also accumulated in these cell types. Vascular bundles in midribs of immature leaf blades contained mRNAs and proteins for both GS1 and PAL abundantly in sclerenchyma cells, although distribution of these two proteins was not completely overlapped. In immature vascular bundles in midribs, lignin deposition was observed in cell walls of xylem parenchyma cells, mestome-sheath cells and sclerenchyma cells. These results implied that a part of GS1 in unexpanded leaf blades is possibly involved in reassimilation of ammonia released from PAL reaction during the lignin production.

Trehalose induces resistance to powdery mildew in wheat

• Reduction in the degree of powdery mildew infection of wheat leaves is observed after treatments with trehalose, a nonreducing disaccharide commonly found in a wide variety of organisms, including fungi. • Wheat (Triticum aestivum) cv. Sideral plants grown in phytotrons were inoculated with Blumeria graminis f.sp. tritici. In addition to degree of infection, the effect of trehalose solution was further investigated using light and fluorescence microscopy and enzyme assays. • Infection in wheat leaves was reduced by 50 and 95% with trehalose solution (15 g l^-1 ) following a single spraying and three sprayings, respectively; in a detached leaf assay, trehalose was effective at concentrations as low as 0.01 g l^-1 . Trehalose did not inhibit conidial germination and differentiation of appressoria (in vitro or on the leaf epidermis), but enhanced papilla deposition in epidermal cells. Trehalose also enhanced phenylalanine ammonia-lyase (PAL) and peroxidase (PO) activities; both markers of plant defence responses. However, the level of three cinnamyl alcohol dehydrogenase (CAD) activities (conyferyl, p-coumaryl and sinapyl alcohol dehydrogenase) was unchanged. • Trehalose treatment of wheat confers resistance to B. graminis infection by activating plant defence responses (e.g. papilla deposition, PAL and PO activities).