Stress responses in alfalfa (Medicago sativa L.) 11. Molecular cloning and expression of alfalfa isoflavone reductase, a key enzyme of isoflavonoid phytoalexin biosynthesis

Biosynthesis and metabolic engineering of isoflavonoids in model plants and crops: a review

Isoflavonoids, the major secondary metabolites within the flavonoid biosynthetic pathway, play important roles in plant defense and exhibit free radical scavenging properties in mammals. Recent advancements in understanding the synthesis, transport, and regulation of isoflavonoids have identified their biosynthetic pathways as promising targets for metabolic engineering, offering potential benefits such as enhanced plant resistance, improved biomass, and restoration of soil fertility. This review provides an overview of recent breakthroughs in isoflavonoid biosynthesis, encompassing key enzymes in the biosynthetic pathway, transporters influencing their subcellular localization, molecular mechanisms regulating the metabolic pathway (including transcriptional and post-transcriptional regulation, as well as epigenetic modifications). Metabolic engineering strategies aimed at boosting isoflavonoid content in both leguminous and non-leguminous plants. Additionally, we discuss emerging technologies and resources for precise isoflavonoid regulation. This comprehensive review primarily focuses on model plants and crops, offering insights for more effective and sustainable metabolic engineering approaches to enhance nutritional quality and stress tolerance.

Phytoestrogens: Chemistry, potential health benefits, and their medicinal importance

Phytoestrogens, also known as xenoestrogens, are secondary metabolites derived from plants that have similar structures and biological effects as human estrogens. These compounds do not directly affect biological functions but can act as agonists or antagonists depending on the level of endogenous estrogen in the body. Phytoestrogens may have an epigenetic mechanism of action independent of estrogen receptors. These compounds are found in more than 300 plant species and are synthesized through the phenylpropanoid pathway, with specific enzymes leading to various chemical structures. Phytoestrogens, primarily phenolic compounds, include isoflavonoids, flavonoids, stilbenes, and lignans. Extensive research in animals and humans has demonstrated the protective effects of phytoestrogens on estrogen-dependent diseases. Clinical trials have also shown their potential benefits in conditions such as osteoporosis, Parkinson's disease, and certain types of cancer. This review provides a concise overview of phytoestrogen classification, chemical diversity, and biosynthesis and discusses the potential therapeutic effects of phytoestrogens, as well as their preclinical and clinical development.

The safflower MBW complex regulates HYSA accumulation through degradation by the E3 ligase CtBB1

The regulatory mechanism of the MBW (MYB-bHLH-WD40) complex in safflower (Carthamus tinctorius) remains unclear. In the present study, we show that the separate overexpression of the genes CtbHLH41, CtMYB63, and CtWD40-6 in Arabidopsis thaliana increased anthocyanin and procyanidin contents in the transgenic plants and partially rescued the trichome reduction phenotype of the corresponding bhlh41, myb63, and wd40-6 single mutants. Overexpression of CtbHLH41, CtMYB63, or CtWD40-6 in safflower significantly increased the content of the natural pigment hydroxysafflor yellow A (HYSA) and negatively regulated safflower petal size. Yeast-two-hybrid, functional, and genetic assays demonstrated that the safflower E3 ligase CtBB1 (BIG BROTHER 1) can ubiquitinate CtbHLH41, marking it for degradation through the 26S proteasome and negatively regulating flavonoid accumulation. CtMYB63/CtWD40-6 enhanced the transcriptional activity of CtbHLH41 on the CtDFR (dihydroflavonol 4-reductase) promoter. We propose that the MBW-CtBB1 regulatory module may play an important role in coordinating HYSA accumulation with other response mechanisms.

Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans

The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.

Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity

Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.

Light-Induced Flavonoid Biosynthesis in Sinopodophyllum hexandrum with High-Altitude Adaptation

Sinopodophyllum hexandrum is a perennial alpine herb producing the anti-cancer metabolite podophyllotoxin (PPT). Although the adaptation of S. hexandrum to high altitudes has been demonstrated and the effects of temperature, precipitation, and UV-B light on plant growth and metabolite accumulation have been studied, knowledge on the role of flavonoid biosynthesis in adapting to high altitudes is limited. In this study, light intensity, amount and type of flavonoids, and differentially expressed proteins (DEPs) and genes (DEGs) at 2300 and 3300 m were analyzed by HPLC, proteomic, transcriptomic, and qRT-PCR analysis. We found that higher light intensity correlated with greater flavonoid, flavonol, and anthocyanin content as well as higher anthocyanin to total flavonoid and flavonol ratios observed at the higher altitude. Based on proteomic and transcriptomic analyses, nine DEPs and 41 DEGs were identified to be involved in flavonoid biosynthesis and light response at 3300 m. The relative expression of nine genes (PAL, CHS1, IFRL, ANS, MYB4, BHLH137, CYP6, PPO1, and ABCB19) involved in flavonoid biosynthesis and seven genes (HSP18.1, HSP70, UBC4, ERF5, ERF9, APX3, and EX2) involved in light stress were observed to be up-regulated at 3300 m compared with 2300 m. These findings indicate that light intensity may play a regulatory role in enhancing flavonoid accumulation that allows S. hexandrum to adapt to elevated-altitude coupled with high light intensity.

The structure characteristics, biosynthesis and health benefits of naturally occurring rare flavonoids

Rare flavonoids, a special subclass of naturally occurring flavonoids with diverse structures including pterocarpans, aurones, neoflavonoids, homoisoflavones, diphenylpropanes, rotenoids and 2-phenylethyl-chromones. They are mainly found in legumes with numerous health benefits. Rare flavonoids are regarded as minor flavonoids due to their very limited abundance in nature. This review gives an overview of the natural occurrences of rare flavonoids from previous literatures. Recent findings on the biosynthesis of rare flavonoids have been updated by describing their structural characteristics and classifications. Recent findings on the health benefits of rare flavonoids have also been compiled and discussed. Natural rare flavonoids with various characteristics from different subclasses from plant-based food sources are stated. They show a wide range of health benefits, including antibacterial, anticancer, anti-osteoporosis and antiviral activities. Studies reviewed suggest that rare flavonoids possessing different skeletons demonstrate different characteristic bioactivities by discussing their mechanism of actions and structure-activity relationships. Besides, recent advances on the biosynthesis of rare flavonoids, such as pterocarpans, rotenoids and aurones are well-known, while the biosynthesis of other subclasses remain unknown. The perspectives and further applications of rare flavonoids using metabolic engineering strategies also be expected.

Elucidation of ustilaginoidin biosynthesis reveals a previously unrecognised class of ene-reductases

Ustilaginoidins are a type of mycotoxin featuring a dimeric naphtho-γ-pyrone skeleton, produced by the rice false smut pathogen Ustilaginoidea virens. Here we used gene disruption, heterologous expression in Aspergillus oryzae, feeding experiments, and in vitro experiments to fully elucidate the biosynthesis of ustilaginoidins. A new route to dimeric 2,3-unsaturated naphtho-γ-pyrones via dimerization of YWA1 (and 3-methyl YWA1) followed by dehydration was discovered. Intriguingly, the reduction of the 2,3-double bond of the pyrenone ring was catalyzed by a phospholipid methyltransferase-like enzyme (UsgR). The reductase was specific for reduction of monomeric, linear naphtho-γ-pyrenones, but not for the dimers. Atroposelective coupling of various monomers by the laccase (UsgL) led to diverse ustilaginoidins. Moreover, 3-epimerism of the 3-methyl-2,3-dihydro-naphtho-γ-pyrones adds additional complexity to the biosynthesis.

The 2,3-double bond reduction of the pyrenone ring in linear naphtho-γ-pyrenones was catalyzed by a phospholipid methyltransferase-like enzyme, namely UsgR, which is a previously unrecognised class of ene-reductases.

Recent Advances in Heterologous Synthesis Paving Way for Future Green-Modular Bioindustries: A Review With Special Reference to Isoflavonoids

Isoflavonoids are well-known plant secondary metabolites that have gained importance in recent time due to their multiple nutraceutical and pharmaceutical applications. In plants, isoflavonoids play a role in plant defense and can confer the host plant a competitive advantage to survive and flourish under environmental challenges. In animals, isoflavonoids have been found to interact with multiple signaling pathways and have demonstrated estrogenic, antioxidant and anti-oncologic activities in vivo. The activity of isoflavonoids in the estrogen pathways is such that the class has also been collectively called phytoestrogens. Over 2,400 isoflavonoids, predominantly from legumes, have been identified so far. The biosynthetic pathways of several key isoflavonoids have been established, and the genes and regulatory components involved in the biosynthesis have been characterized. The biosynthesis and accumulation of isoflavonoids in plants are regulated by multiple complex environmental and genetic factors and interactions. Due to this complexity of secondary metabolism regulation, the export and engineering of isoflavonoid biosynthetic pathways into non-endogenous plants are difficult, and instead, the microorganisms Saccharomyces cerevisiae and Escherichia coli have been adapted and engineered for heterologous isoflavonoid synthesis. However, the current ex-planta production approaches have been limited due to slow enzyme kinetics and traditionally laborious genetic engineering methods and require further optimization and development to address the required titers, reaction rates and yield for commercial application. With recent progress in metabolic engineering and the availability of advanced synthetic biology tools, it is envisaged that highly efficient heterologous hosts will soon be engineered to fulfill the growing market demand.

Molecular cloning and biochemical characterization of isoflav-3-ene synthase, a key enzyme of the biosyntheses of (+)-pisatin and coumestrol

Most leguminous plants produce (-)-type enantiomers of pterocarpans as the phytoalexin, but pea (Pisum sativum L.) produces the opposite stereoisomer of pterocarpan, (+)-pisatin. Biosynthesis of (-)-pterocarpan skeleton is completely characterized at the molecular level, and pterocarpan synthase (PTS), a dirigent (DIR) domain-containing protein, participates in the last dehydration reaction. Similarly, isoflav-3-ene, a precursor of (+)-pisatin, is likely to be biosynthesized by the DIR-mediated dehydration reaction; however the biosynthesis is still unknown. In the present study, we screened PTS homologs based on RNA-sequence data from (+)-pisatin-producing pea seedlings and demonstrated that one of the candidates encodes isoflav-3-ene synthase (I3S). Real-time PCR analysis revealed that transcripts of I3S, in addition to other genes involved in the (+)-pisatin pathway, transiently accumulated in pea upon elicitation prior to the maximum accumulation of (+)-pisatin. I3S orthologs were also found in soybean and Lotus japonicus that are not known to accumulate (+)-pterocarpan, and the catalytic function of gene products was verified to be I3S by the in vitro enzyme assay. Incubation of the crude extract of elicited soybean cells with isoflav-3-ene yielded coumestrol, suggesting that isoflav-3-ene is a precursor of coumestrol biosynthesis in soybean.

The Involvement of Jasmonic Acid, Ethylene, and Salicylic Acid in the Signaling Pathway of Clonostachys rosea-Induced Resistance to Gray Mold Disease in Tomato

Tomato gray mold disease caused by Botrytis cinerea is a serious disease that threatens tomato production around the world. Clonostachys rosea has been used successfully as a biocontrol agent against divergent plant pathogens, including B. cinerea. To understand the signal transduction pathway of C. rosea-induced resistance to tomato gray mold disease, the effects of C. rosea on gray mold tomato leaves along with changes in the activities of three defense enzymes (phenylalanine ammonialyase [PAL], polyphenol oxidase [PPO], and catalase [CAT]), second messengers (nitric oxide [NO], hydrogen peroxide [H₂O₂], and superoxide anion radical [O₂^-]), and stress-related genes (mitogen-activated protein kinase [MAPK], WRKY, Lexyl2, and atpA) in four different hormone-deficient (jasmonic acid [JA], ethylene [ET], salicylic acid [SA], and gibberellin) tomato mutants were investigated. The results revealed that C. rosea significantly inhibited the growth of mycelia and spore germination of B. cinerea. Furthermore, it reduced the incidence of gray mold disease, induced higher levels of PAL and PPO, and induced lower levels of CAT activities in tomato leaves. Moreover, it also increased NO, H₂O₂, and O₂^- levels and the gene expression levels of WRKY, MAPK, atpA, and Lexyl2. The incidence of gray mold disease in four hormone-deficient mutants was higher than that in the corresponding wild-type tomato plants. Among all of these hormone-deficient tomato mutants, JA had the most significant effect in regulating the different signal molecules. Additional study suggested that JA upregulated the expression of Lexyl2, MAPK, and WRKY but downregulated atpA. Furthermore, JA also enhanced the activity of PAL, PPO, and CAT and the production of NO and H₂O₂. SA downregulated CAT and PAL, whereas ET upregulated PAL but downregulated CAT. This study is of significance in understanding the regulatory pathways and biocontrol mechanism of C. rosea against B. cinerea.

Knock-Down of the IFR1 Protein Perturbs the Homeostasis of Reactive Electrophile Species and Boosts Photosynthetic Hydrogen Production in Chlamydomonas reinhardtii

The protein superfamily of short-chain dehydrogenases/reductases (SDR), including members of the atypical type (aSDR), covers a huge range of catalyzed reactions and in vivo substrates. This superfamily also comprises isoflavone reductase-like (IRL) proteins, which are aSDRs highly homologous to isoflavone reductases from leguminous plants. The molecular function of IRLs in non-leguminous plants and green microalgae has not been identified as yet, but several lines of evidence point at their implication in reactive oxygen species homeostasis. The Chlamydomonas reinhardtii IRL protein IFR1 was identified in a previous study, analyzing the transcriptomic changes occurring during the acclimation to sulfur deprivation and anaerobiosis, a condition that triggers photobiological hydrogen production in this microalgae. Accumulation of the cytosolic IFR1 protein is induced by sulfur limitation as well as by the exposure of C. reinhardtii cells to reactive electrophile species (RES) such as reactive carbonyls. The latter has not been described for IRL proteins before. Over-accumulation of IFR1 in the singlet oxygen response 1 (sor1) mutant together with the presence of an electrophile response element, known to be required for SOR1-dependent gene activation as a response to RES, in the promoter of IFR1, indicate that IFR1 expression is controlled by the SOR1-dependent pathway. An implication of IFR1 into RES homeostasis, is further implied by a knock-down of IFR1, which results in a diminished tolerance toward RES. Intriguingly, IFR1 knock-down has a positive effect on photosystem II (PSII) stability under sulfur-deprived conditions used to trigger photobiological hydrogen production, by reducing PSII-dependent oxygen evolution, in C. reinhardtii. Reduced PSII photoinhibition in IFR1 knock-down strains prolongs the hydrogen production phase resulting in an almost doubled final hydrogen yield compared to the parental strain. Finally, IFR1 knock-down could be successfully used to further increase hydrogen yields of the high hydrogen-producing mutant stm6, demonstrating that IFR1 is a promising target for genetic engineering approaches aiming at an increased hydrogen production capacity of C. reinhardtii cells.

De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages

Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) is a traditional medicinal herb in the family Liliaceae that has significant pharmacological effects on immunity and cardiovascular disease. In this study, three different growth stages of Zhe-Maidong were investigated using RNA-seq, and a total of 16.4 Gb of raw data was obtained. After filtering and assembling, 96,738 unigenes with an average length of 605.3 bp were ultimately generated. A total of 77,300 unigenes were annotated using information from five databases, including the NT, NR, SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Additionally, the mechanisms of flavonoid, saponin and polysaccharide biosynthesis and of accumulation at different stages of tuber development were also characterized. From the first to third years, the contents of flavonoids, saponins and polysaccharides all increased, whereas the expression levels of related genes decreased in the flavonoid and saponin pathways and first increased and then decreased in the polysaccharide pathway. The results of this study provide the most comprehensive expressed sequence resource for Zhe-Maidong and will expand the available O. japonicus gene library and facilitate further genome-wide research and analyses of this species.

The Missing Link in Leguminous Pterocarpan Biosynthesis is a Dirigent Domain-Containing Protein with Isoflavanol Dehydratase Activity

Pterocarpan forms the basic structure of leguminous phytoalexins, and most of the isoflavonoid pathway genes encoding the enzymes responsible for its biosynthesis have been identified. However, the last step of pterocarpan biosynthesis is a ring closure reaction, and the enzyme that catalyzes this step, 2'-hydroxyisoflavanol 4,2'-dehydratase or pterocarpan synthase (PTS), remains as an unidentified 'missing link'. This last ring formation is assumed to be the key step in determining the stereochemistry of pterocarpans, which plays a role in their antimicrobial activity. In this study, a cDNA clone encoding PTS from Glycyrrhiza echinata (GePTS1) was identified through functional expression fractionation screening of a cDNA library, which requires no sequence information, and orthologs from soybean (GmPTS1) and Lotus japonicus (LjPTS1) were also identified. These proteins were heterologously expressed in Escherichia coli and biochemically characterized. Surprisingly, the proteins were found to include amino acid motifs characteristic of dirigent proteins, some of which control stereospecific phenoxy radical coupling in lignan biosynthesis. The stereospecificity of substrates and products was examined using four substrate stereoisomers with hydroxy and methoxy derivatives at C-4'. The results showed that the 4R configuration was essential for the PTS reaction, and (-)- and (+)-pterocarpans were produced depending on the stereochemistry at C-3. In suspension-cultured soybean cells, levels of the GmPTS1 transcript increased temporarily prior to the peak in phytoalexin accumulation, strongly supporting the possible involvement of PTS in pterocarpan biosynthesis.

Expression and functional analyses of a putative phenylcoumaran benzylic ether reductase in Arabidopsis thaliana

A candidate gene for phenylcoumaran benzylic ether reductase in Arabidopsis thaliana encodes a peptide with predicted functional activity and plays a crucial role in secondary metabolism. Phenylcoumaran benzylic ether reductase (PCBER) is thought to be an enzyme crucial in the biosynthesis of 8-5'-linked neolignans. Genes of the enzyme have been isolated and characterized in several plant species. In this study, we cloned cDNA and the 5'-untranslated region of one PCBER candidate gene (At4g39230, designated AtPCBER1) from Arabidopsis thaliana. At the amino acid level, AtPCBER1 shows high sequence identity (64-71 %) with PCBERs identified from other plant species. Expression analyses of AtPCBER1 by reverse transcriptase-polymerase chain reaction and histochemical analysis of transgenic plants harboring the 5'-untranslated region of AtPCBER1 linked with gus coding sequence indicate that expression is induced by wounding and is expressed in most tissues, including flower, stem, leaf, and root. Catalytic analysis of recombinant AtPCBER1 with neolignan and lignans in the presence of NADPH suggests that the protein can reduce not only the 8-5'-linked neolignan, dehydrodiconiferyl alcohol, but also 8-8' linked lignans, pinoresinol, and lariciresinol, with lower activities. To investigate further, we performed metabolomic analyses of transgenic plants in which the target gene was up- or down-regulated. Our results indicate no significant effects of AtPCBER1 gene regulation on plant growth and development; however, levels of some secondary metabolites, including lignans, flavonoids, and glucosinolates, differ between wild-type and transgenic plants. Taken together, our findings indicate that AtPCBER1 encodes a polypeptide with PCBER activity and has a critical role in the biosynthesis of secondary metabolites in A. thaliana.

Overexpression of Soybean Isoflavone Reductase (GmIFR) Enhances Resistance to Phytophthora sojae in Soybean

Isoflavone reductase (IFR) is an enzyme involved in the biosynthetic pathway of isoflavonoid phytoalexin in plants. IFRs are unique to the plant kingdom and are considered to have crucial roles in plant response to various biotic and abiotic environmental stresses. Here, we report the characterization of a novel member of the soybean isoflavone reductase gene family GmIFR. Overexpression of GmIFR transgenic soybean exhibited enhanced resistance to Phytophthora sojae. Following stress treatments, GmIFR was significantly induced by P. sojae, ethephon (ET), abscisic acid (placeCityABA), salicylic acid (SA). It is located in the cytoplasm when transiently expressed in soybean protoplasts. The daidzein levels reduced greatly for the seeds of transgenic plants, while the relative content of glyceollins in transgenic plants was significantly higher than that of non-transgenic plants. Furthermore, we found that the relative expression levels of reactive oxygen species (ROS) of transgenic soybean plants were significantly lower than those of non-transgenic plants after incubation with P. sojae, suggesting an important role of GmIFR might function as an antioxidant to reduce ROS in soybean. The enzyme activity assay suggested that GmIFR has isoflavone reductase activity.

Expression profiles of defence related cDNAs in oil palm (Elaeis guineensis Jacq.) inoculated with mycorrhizae and Trichoderma harzianum Rifai T32

Basal stem rot is one of the major diseases of oil palm (Elaies guineensis Jacq.) caused by pathogenic Ganoderma species. Trichoderma and mycorrhizae were proposed to be able to reduce the disease severity. However, their roles in improving oil palm defence system by possibly inducing defence-related genes in the host are not well characterized. To better understand that, transcript profiles of eleven putative defence-related cDNAs in the roots of oil palm inoculated with Trichoderma harzianum T32 and mycorrhizae at different time points were studied. Transcripts encoding putative Bowman-Birk protease inhibitor (EgBBI2) and defensin (EgDFS) increased more than 2 fold in mycorrhizae-treated roots at 6 weeks post inoculation (wpi) compared to those in controls. Transcripts encoding putative dehydrin (EgDHN), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), type 2 ribosome inactivating protein (EgT2RIP), and EgDFS increased in the oil palm roots treated with T. harzianum at 6 and/or 12 wpi compared to those in the controls. Some of these genes were also expressed in oil palm roots treated with Ganoderma boninense. This study provides an insight of some defence-related genes induced by Trichoderma and mycorrhizae, and their roles as potential agents to boost the plant defence system.

RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress

Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resulted in 94.3 to 95.3% of the unmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were unigene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were "response to external stimulus" and "electron-carrier activity". Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.

Effect of lead treatment on medicarpin accumulation and on the gene expression of key enzymes involved in medicarpin biosynthesis in Medicago sativa L

Lead (Pb) is the most common heavy metal contaminant in the environment. The present study was undertaken to determine the effect of Pb treatment on medicarpin production and accumulation in Medicago sativa L. To this aim, 7- and 30-day-old plants were treated with 0, 120, 240, 500, and 1,000 μM Pb during 10 days. The content of medicarpin was determined by HPLC, and the extent of medicarpin production was deduced from the result of semiquantitative RT-PCR performed on PAL, CHS, and VR genes. HPLC results indicated that medicarpin concentration has been reduced in the roots, while its exudation to the culture medium has been increased. RT-PCR results indicated that the transcript levels of PAL, CHS, and VR genes have not been affected following Pb stress in seedlings. At the vegetative stage, transcript levels of PAL and CHS genes have been reduced in the roots. However, the transcript level of VR gene increased at 120 and 240 μM Pb, while it decreased at higher concentrations. In the shoot, the transcript levels of PAL, CHS, and VR genes were increased following increased concentration of lead in the medium. Overall, q-PCR results suggest that medicarpin biosynthesis has been induced in the shoots and reduced in the roots of the plants treated with a toxic concentration of Pb.

Carbon-carbon double-bond reductases in nature

Reduction of C = C bonds by reductases, found in a variety of microorganisms (e.g. yeasts, bacteria, and lower fungi), animals, and plants has applications in the production of metabolites that include pharmacologically active drugs and other chemicals. Therefore, the reductase enzymes that mediate this transformation have become important therapeutic targets and biotechnological tools. These reductases are broad-spectrum, in that, they can act on isolation/conjugation C = C-bond compounds, α,β-unsaturated carbonyl compounds, carboxylic acids, acid derivatives, and nitro compounds. In addition, several mutations in the reductase gene have been identified, some associated with diseases. Several of these reductases have been cloned and/or purified, and studies to further characterize them and determine their structure in order to identify potential industrial biocatalysts are still in progress. In this study, crucial reductases for bioreduction of C = C bonds have been reviewed with emphasis on their principal substrates and effective inhibitors, their distribution, genetic polymorphisms, and implications in human disease and treatment.

Bioconversion of pinoresinol into matairesinol by use of recombinant Escherichia coli

Lignans, a class of dimeric phenylpropanoid derivative found in plants, such as whole grains and sesame and flax seeds, have anticancer activity and can act as phytoestrogens. The lignans secoisolariciresinol and matairesinol can be converted in the mammalian proximal colon into enterolactone and enterodiol, respectively, which reduce the risk of breast and colon cancer. To establish an efficient bioconversion system to generate matairesinol from pinoresinol, the genes encoding pinoresinol-lariciresinol reductase (PLR) and secoisolariciresinol dehydrogenase (SDH) were cloned from Podophyllum pleianthum Hance, an endangered herb in Taiwan, and the recombinant proteins, rPLR and rSDH, were expressed in Escherichia coli and purified. The two genes, termed plr-PpH and sdh-PpH, were also linked to form two bifunctional fusion genes, plr-sdh and sdh-plr, which were also expressed in E. coli and purified. Bioconversion in vitro at 22°C for 60 min showed that the conversion efficiency of fusion protein PLR-SDH was higher than that of the mixture of rPLR and rSDH. The percent conversion of (+)-pinoresinol to matairesinol was 49.8% using PLR-SDH and only 17.7% using a mixture of rPLR and rSDH. However, conversion of (+)-pinoresinol by fusion protein SDH-PLR stopped at the intermediate product, secoisolariciresinol. In vivo, (+)-pinoresinol was completely converted to matairesinol by living recombinant E. coli expressing PLR-SDH without addition of cofactors.

(+)-Pisatin biosynthesis: from (-) enantiomeric intermediates via an achiral 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene

(+)-Pisatin, produced by peas (Pisum sativum L.), is an isoflavonoid derivative belonging to the pterocarpan family. It was the first chemically identified phytoalexin, and subsequent research has demonstrated that most legumes produce pterocarpans with the opposite stereochemistry. Studies on the biosynthesis of (+)-pisatin have shown that (-) enantiomeric compounds are intermediates in (+)-pisatin synthesis. However, the steps from the (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanone [(-)-sophorol] intermediate to (+)-6a-hydroxymaackiain intermediate are undetermined. Chemical reduction of (-)-sophorol using sodium borohydride (NaBH4) produced two isomers of (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanol [(-)-DMDI] with optimal UV absorbance at 299.3 and 300.5 nm, respectively. In contrast, enzymatic reduction of (-)-sophorol by the pea enzyme sophorol reductase (SOR) produced only the 299.3 nm (-)-DMDI isomer. Proton nuclear magnetic resonance ((1)H NMR) analysis of the 299.3 nm (-)-DMDI isomer demonstrated that this isomer had the same NMR spectrum as previously reported for cis-isoflavanol isomers, indicating that cis-(-)-DMDI is an intermediate in (+)-pisatin biosynthesis. Enzyme assays using protein extracts from pea tissue treated with CuCl2 as an elicitor converted the cis-(-)-DMDI isomer into an achiral isoflavene, 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and the trans-(-)-DMDI isomer was not metabolized by the same protein preparation. A comparison of the enzyme activities on cis-(-)-DMDI with protein preparations from elicited tissue versus non-elicited tissue showed a threefold increase in the amount of activity in the proteins from the elicited tissue. Proteins from the elicited tissues of alfalfa, bean, and chickpea converted cis-(-)-DMDI into either (-)-maackiain and/or (-)-sophorol, while proteins from the elicited tissues of broccoli and pepper produced no detectable product. These results are consistent with the involvement of cis-(-)-DMDI and the achiral DMDIF as intermediates in (+)-pisatin biosynthesis.

Role of plant defence in alfalfa during symbiosis

During effective symbiosis, rhizobia colonize their hosts, and avoid plant defence mechanisms. To determine whether the host defence responses can be elicited by the symbiotic bacteria, specific markers involved in incompatible pathogenic interactions are required. The available markers of alfalfa defence mechanisms are described and their use in the study of the symbiotic interaction discussed. As defence-related gene expression in roots is not always related to defence mechanisms, other model systems have been established allowing confirmation of an important role of bacterial surface components in alfalfa-Rhizobium meliloti interactions. Nod factors at high concentrations have been shown to elicit defence-like responses in Medicago cell suspensions and roots. Elicitation of defence mechanisms by high levels of Nod factors in Rhizobium-infected roots may be a part of the mechanism by which nodulation is feed-back regulated.

Allyl/propenyl phenol synthases from the creosote bush and engineering production of specialty/commodity chemicals, eugenol/isoeugenol, in Escherichia coli

The creosote bush (Larrea tridentata) harbors members of the monolignol acyltransferase, allylphenol synthase, and propenylphenol synthase gene families, whose products together are able to catalyze distinct regiospecific conversions of various monolignols into their corresponding allyl- and propenyl-phenols, respectively. In this study, co-expression of a monolignol acyltransferase with either substrate versatile allylphenol or propenylphenol synthases in Escherichia coli established that various monolignol substrates were efficiently converted into their corresponding allyl/propenyl phenols, as well as providing proof of concept for efficacious conversion in a bacterial platform. This capability thus potentially provides an alternate source to these important plant phytochemicals, whether for flavor/fragrance and fine chemicals, or ultimately as commodities, e.g., for renewable energy or other intermediate chemical purposes. Previous reports had indicated that specific and highly conserved amino acid residues 84 (Phe or Val) and 87 (Ile or Tyr) of two highly homologous allyl/propenyl phenol synthases (circa 96% identity) from a Clarkia species mainly dictate their distinct regiospecific catalyzed conversions to afford either allyl- or propenyl-phenols, respectively. However, several other allyl/propenyl phenol synthase homologs isolated by us have established that the two corresponding amino acid 84 and 87 residues are not, in fact, conserved.

Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen

Isoflavone reductase-like proteins (IRLs) are enzymes with key roles in the metabolism of diverse flavonoids. Last identified olive pollen allergen (Ole e 12) is an IRL relevant for allergy amelioration, since it exhibits high prevalence among atopic patients. The goals of this study are the characterization of (A) the structural-functionality of Ole e 12 with a focus in its catalytic mechanism, and (B) its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering (1) physicochemical properties and functional-regulatory motifs, (2) sequence analysis, 2-D and 3D structural homology modeling comparative study and molecular docking, (3) conservational and evolutionary analysis, (4) catalytic mechanism modeling, and (5) sequence, structure-docking based B-cell epitopes prediction, while T-cell epitopes were predicted by inhibitory concentration and binding score methods. Structural-based detailed features, phylogenetic and sequences analysis have identified Ole e 12 as phenylcoumaran benzylic ether reductase. A catalytic mechanism has been proposed for Ole e 12 which display Lys133 as one of the conserved residues of the IRLs catalytic tetrad (Asn-Ser-Tyr-Lys). Structure characterization revealed a conserved protein folding among plants IRLs. However, sequence polymorphism significantly affected residues involved in the catalytic pocket structure and environment (cofactor and substrate interaction-recognition). It might also be responsible for IRLs isoforms functionality and regulation, since micro-heterogeneities affected physicochemical and posttranslational motifs. This polymorphism might have large implications for molecular differences in B- and T-cells epitopes of Ole e 12, and its identification may help designing strategies to improve the component-resolving diagnosis and immunotherapy of pollen and food allergy through development of molecular tools.

Proteomic analysis of Fusarium oxysporum f. sp. cubense tropical race 4-inoculated response to Fusarium wilts in the banana root cells

BACKGROUND

Fusarium wilt of banana is one of the most destructive diseases in the world. This disease has caused heavy losses in major banana production areas. Except for molecular breeding methods based on plant defense mechanisms, effective methods to control the disease are still lacking. Dynamic changes in defense mechanisms between susceptible, moderately resistant, and highly resistant banana and Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4) at the protein level remain unknown. This research reports the proteomic profile of three banana cultivars in response to Foc4 and transcriptional levels correlated with their sequences for the design of disease control strategies by molecular breeding.

RESULTS

Thirty-eight differentially expressed proteins were identified to function in cell metabolism. Most of these proteins were positively regulated after Foc4 inoculation. These differentially regulated proteins were found to have important functions in banana defense response. Functional categories implicated that these proteins were associated with pathogenesis-related (PR) response; isoflavonoid, flavonoid, and anthocyanin syntheses; cell wall strengthening; cell polarization; reactive oxygen species production and scavenging; jasmonic acid-, abscisic acid-, and auxin-mediated signaling conduction; molecular chaperones; energy; and primary metabolism. By comparing the protein profiles of resistant and susceptible banana cultivars, many proteins showed obvious distinction in their defense mechanism functions. PR proteins in susceptible 'Brazil' were mainly involved in defense. The proteins related to PR response, cell wall strengthening and antifungal compound synthesis in moderately resistant 'Nongke No.1' were mainly involved in defense. The proteins related to PR response, cell wall strengthening, and antifungal compound synthesis in highly resistant 'Yueyoukang I' were mainly involved in defense. 12 differentially regulated genes were selected to validate through quantitative real time PCR method. Quantitative RT-PCR analyses of these selected genes corroborate with their respective protein abundance after pathogen infection.

CONCLUSIONS

This report is the first to use proteomic profiling to study the molecular mechanism of banana roots infected with Foc4. The differentially regulated proteins involved in different defense pathways are likely associated with different resistant levels of the three banana cultivars.

Expression patterns of an isoflavone reductase-like gene and its possible roles in secondary metabolism in Ginkgo biloba

Our results showed that GbIRL1 belongs to the PCBER protein family. Besides, IRL1 gene was a novel gene regulating lignin change and also effecting the accumulation of flavonoids in Ginkgo. A cDNA encoding the IFR-like protein was isolated from the leaves of Ginkgo biloba L., designated as GbIRL1 (Accession no. KC244282). The cDNA of GbIRL1 was 1,203 bp containing a 921 bp open reading frame encoding a polypeptide of 306 amino acids. Comparative and bioinformatic analyses revealed that GbIRL1 showed extensive homology with IFLs from other gymnosperm species. Phylogenetic tree analysis revealed that GbIRL1 shared the same ancestor in evolution with other PCBERs protein and had a further relationship with other gymnosperm species. The recombinant protein was successfully expressed in E. coli strain with pET-28a vector. The vitro enzyme activity assay by HPLC indicated that recombinant GbIRL1 protein could catalyze the formation the TDDC, IDDDC from DDDC, DDC. Tissue expression pattern analysis showed that GbIRL1 was constitutively expressed in stem and roots, especially in the parts of the pest and fungal infection, with the lower expression being found in 1- or 2-year old stem. The increased expression of GbIRL1 was detected when the seedlings were treated with Ultraviole-B, ALA, wounding and ethephon, abscisic acid, salicylic acid. Correlation analysis between GbIRL1 activity and flavonoid accumulation during Ginkgo leaf growth indicated that GbIRL1 might be the rate-limiting enzyme in the biosynthesis pathway of flavonoids in Ginkgo leaves. Results of RT-PCR analysis showed that the transcription level of change in GbIRL1 power correlated with flavonoid contents, suggesting IRL1 gene as a novel gene regulating lignin change and also effecting the accumulation of flavonoids in Ginkgo.

Synthesis, optical resolution, absolute configuration, and osteogenic activity of cis-pterocarpans

A convenient synthesis of natural and synthetic pterocarpans was achieved in three steps. Optical resolution of the respective enantiomers was accomplished by analytical and semi-preparative HPLC on a chiral stationary phase. For medicarpin and its synthetic derivative 9-demethoxymedicarpin, the absolute configuration was confirmed by a combination of experimental LC-ECD coupling and quantum-chemical ECD calculations. (-)-Medicarpin and (-)-9-demethoxymedicarpin are both 6aR,11aR-configured, and consequently the corresponding enantiomers, (+)-medicarpin and (+)-9-demethoxymedicarpin, possess the 6aS,11aS-configuration. A comparative mechanism study for osteogenic (bone forming) activity of medicarpin (racemic versus enantiomerically pure material) revealed that (+)-(6aS,11aS)-medicarpin (6a) significantly increased the bone morphogenetic protein-2 (BMP2) expression and the level of the bone-specific transcription factor Runx-2 mRNA, while the effect was opposite for the other enantiomer, (-)-(6aR,11aR)-medicarpin (6a), and for the racemate, (±)-medicarpin, the combined effect of both the enantiomers on transcription levels was observed.

Enantiomeric natural products: occurrence and biogenesis

In nature, chiral natural products are usually produced in optically pure form-however, occasionally both enantiomers are formed. These enantiomeric natural products can arise from a single species or from different genera and/or species. Extensive research has been carried out over the years in an attempt to understand the biogenesis of naturally occurring enantiomers; however, many fascinating puzzles and stereochemical anomalies still remain.

Proteomic analysis of young leaves at three developmental stages in an albino tea cultivar

Background

White leaf No.1 is a typical albino tea cultivar grown in China and it has received increased attention in recent years due to the fact that white leaves containing a high level of amino acids, which are very important components affecting the quality of tea drink. According to the color of its leaves, the development of this tea cultivar is divided into three stages: the pre-albinistic stage, the albinistic stage and the regreening stage. To understand the intricate mechanism of periodic albinism, a comparative proteomic approach based on two-dimensional electrophoresis (2-DE) and mass spectrometry was adopted first time to identify proteins that changed in abundance during the three developmental periods.

Results

The 2-DE results showed that the expression level of 61 protein spots varied markedly during the three developmental stages. To analyze the functions of the significantly differentially expressed protein spots, 30 spots were excised from gels and analyzed by matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry. Of these, 26 spots were successfully identified. All identified protein spots were involved in metabolism of carbon, nitrogen and sulfur, photosynthesis, protein processing, stress defense and RNA processing, indicating these physiological processes may play crucial roles in the periodic albinism. Quantitative real-time RT-PCR analysis was used to assess the transcriptional level of differentially expressed proteins. In addition, the ultrastructural studies revealed that the etioplast-chloroplast transition in the leaf cell of White leaf No. 1 was inhibited and the grana in the chloroplast was destroyed at the albinistic stage.

Conclusions

In this work, the proteomic analysis revealed that some proteins may have important roles in the molecular events involved in periodic albinism of White leaf No. 1 and identificated many attractive candidates for further investigation. In addition, the ultrastructural studies revealed that the change in leaf color of White leaf No. 1 might be a consequence of suppression of the etioplast-chloroplast transition and damage to grana in the chloroplast induced by temperature. These results provide much useful information to improve our understanding of the mechanism of albinism in the albino tea cultivar.

Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

BACKGROUND

Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation.

RESULTS

A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes.

CONCLUSION

Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.

Genome-wide analysis of phenylpropanoid defence pathways

Phenylpropanoids can function as preformed and inducible antimicrobial compounds, as well as signal molecules, in plant-microbe interactions. Since we last reviewed the field 8 years ago, there has been a huge increase in our understanding of the genes of phenylpropanoid biosynthesis and their regulation, brought about largely by advances in genome technology, from whole-genome sequencing to massively parallel gene expression profiling. Here, we present an overview of the biosynthesis and roles of phenylpropanoids in plant defence, together with an analysis of confirmed and predicted phenylpropanoid pathway genes in the sequenced genomes of 11 plant species. Examples are provided of phylogenetic and expression clustering analyses, and the large body of underlying genomic data is provided through a website accessible from the article.

Overexpression of rice isoflavone reductase-like gene (OsIRL) confers tolerance to reactive oxygen species

Isoflavone reductase is an enzyme involved in isoflavonoid biosynthesis in plants. However, rice isoflavone reductase-like gene (OsIRL, accession no. AY071920) has not been unraveled so far. Here, we have characterized its behavior in response to oxidizing agents. Using Northern and Western blot analyses, the OsIRL gene and protein were shown to be down-regulated in young seedling roots treated with reduced glutathione (GSH) and diphenyleneiodonium (DPI), known quenchers of reactive oxygen species (ROS). The OsIRL transcript level in rice suspension-cultured cells was also found to be induced by oxidants such as hydrogen peroxide (H(2)O(2)), ferric chloride (FeCl(3)), methyl viologen (MV) and glucose/glucose oxidase (G/GO), but down-regulated when co-treated with GSH. Furthermore, to investigate whether overexpression of OsIRL in transgenic rice plants promotes resistance to ROS, we generated transgenic rice lines overexpressing the OsIRL gene under an abscisic acid (ABA) inducible promoter. Results showed that the OsIRL transgenic rice line activated by ABA treatment was tolerant against MV and G/GO-induced stress in rice leave and suspension-cultured cells. Our results strongly suggest the involvement of OsIRL in homeostasis of ROS.

Stimulation of nodulation in Medicago truncatula by low concentrations of ammonium: quantitative reverse transcription PCR analysis of selected genes

Although mineral nitrogen generally has negative effects on nodulation in legume-rhizobia symbioses, low concentrations of ammonium stimulate nodulation in some legumes. In this study, the effects of ammonium and nitrate on growth, nodulation and expression of 2 nitrogen transport and 12 putative nodulation-related genes of the model symbiosis of Medicago truncatula - Sinorhizobium meliloti are investigated. After 3 weeks of hydroponic growth, whole-plant nodulation was enhanced in all the ammonium treatments and up to three-fold in the 0.5 mM treatment compared with the zero-nitrogen control. Specific nodulation (nodules g(-1) root dry weight) was greatly stimulated in the 0.1 and 0.5 mM NH4+ treatments, to a lower extent in the 0.1 mM NO3- treatment, and inhibited in all other treatments. Expression of the 14 selected genes was observed at 0, 6, 12 and 24 h after exposure to rhizobia and nitrogen. Expression of nitrogen transporter genes increased significantly, but responses of the three genes putatively associated with symbiosis signaling/nodule initiation were mixed. There were infrequent responses of genes coding for an ABA-activated protein kinase or a gibberellin-regulated protein, but an ethylene-responsive element-binding factor showed increased expression in various treatments and sampling times. Three auxin-responsive genes and three cytokinin-responsive genes showed varied responses to ammonium and nitrate. This study indicates that low concentrations of ammonium stimulate nodulation in M. truncatula, but the data were inconclusive in verifying the hypothesis that a relatively high ratio of cytokinin to auxin in roots may be an underlying mechanism in this stimulation of nodulation.

Inactivation of pea genes by RNAi supports the involvement of two similar O-methyltransferases in the biosynthesis of (+)-pisatin and of chiral intermediates with a configuration opposite that found in (+)-pisatin

(+)-Pisatin, the major phytoalexin of pea (Pisum sativum L.), is believed to be synthesized via two chiral intermediates, (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanone [(-)-sophorol] and (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanol [(-)-DMDI]; both have an opposite C-3 absolute configuration to that found at C-6a in (+)-pisatin. The expression of isoflavone reductase (IFR), which converts 7,2'-dihydroxy-4',5'-methylenedioxyisoflavone (DMD) to (-)-sophorol, sophorol reductase (SOR), which converts (-)-sophorol to (-)-DMDI, and hydroxymaackiain-3-O-methyltransferase (HMM), believed to be the last step of (+)-pisatin biosynthesis, were inactivated by RNA-mediated genetic interference (RNAi) in pea hairy roots. Some hairy root lines containing RNAi constructs of IFR and SOR accumulated DMD or (-)-sophorol, respectively, and were deficient in (+)-pisatin biosynthesis supporting the involvement of chiral intermediates with a configuration opposite to that found in (+)-pisatin in the biosynthesis of (+)-pisatin. Pea proteins also converted (-)-DMDI to an achiral isoflavene suggesting that an isoflavene might be the intermediate through which the configuration is changed to that found in (+)-pisatin. Hairy roots containing RNAi constructs of HMM also were deficient in (+)-pisatin biosynthesis, but did not accumulate (+)-6a-hydroxymaackiain, the proposed precursor to (+)-pisatin. Instead, 2,7,4'-trihydroxyisoflavanone (TIF), daidzein, isoformononetin, and liquiritigenin accumulated. HMM has a high amino acid similarity to hydroxyisoflavanone-4'-O-methyltransferase (HI4'OMT), an enzyme that methylates TIF, an early intermediate in the isoflavonoid pathway. The accumulation of these four compounds is consistent with the blockage of the synthesis of (+)-pisatin at the HI4'OMT catalyzed step resulting in the accumulation of liquiritigenin and TIF and the diversion of the pathway to produce daidzein and isoformononetin, compounds not normally made by pea. Previous results have identified two highly similar "HMMs" in pea. The current results suggest that both of these O-methyltransferases are involved in (+)-pisatin biosynthesis and that one functions early in the pathway as HI4'OMT and the second acts at the terminal step of the pathway.

A proteomic analysis of rice seedlings responding to 1,2,4-trichlorobenzene stress

The proteomic analysis of rice (Oryza sativa L.) roots and leaves responding to 1,2,4-trichlorobenzene (TCB) stress was carried out by two dimensional gel electrophoresis, mass spectrometric (MS), and protein database analysis. The results showed that 5 mg/L TCB stress had a significant effect on global proteome in rice roots and leaves. The analysis of the category and function of TCB stress inducible proteins showed that different kinds of responses were produced in rice roots and leaves, when rice seedlings were exposed to 5 mg/L TCB stress. Most responses are essential for rice defending the damage of TCB stress. These responses include detoxication of toxic substances, expression of pathogenesis-related proteins, synthesis of cell wall substances and secondary compounds, regulation of protein and amino acid metabolism, activation of methionine salvage pathway, and also include osmotic regulation and phytohormone metabolism. Comparing the TCB stress inducible proteins between the two cultivars, the beta-glucosidase and pathogenesis-related protein family 10 proteins were particularly induced by TCB stress in the roots of rice cultivar (Oryza sativa L.) Aizaizhan, and the glutathione S-transferase and aci-reductone dioxygenase 4 were induced in the roots of rice cultivar Shanyou 63. This may be one of the important mechanisms for Shanyou 63 having higher tolerance to TCB stress than Aizaizhan.

Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate

* Herbivore-induced plant volatiles (HIPVs), in addition to attracting natural enemies of herbivores, can serve a signaling function within plants to induce or prime defenses. However, it is largely unknown, particularly in woody plants, which volatile compounds within HIPV blends can act as signaling molecules. * Leaves of hybrid poplar saplings were exposed in vivo to naturally wound-emitted concentrations of the green leaf volatile (GLV) cis-3-hexenyl acetate (z3HAC) and then subsequently fed upon by gypsy moth larvae. Volatiles were collected throughout the experiments, and leaf tissue was collected to measure phytohormone concentrations and expression of defense-related genes. * Relative to controls, z3HAC-exposed leaves had higher concentrations of jasmonic acid and linolenic acid following gypsy moth feeding. Furthermore, z3HAC primed transcripts of genes that mediate oxylipin signaling and direct defenses, as determined by both qRT-PCR and microarray analysis using the AspenDB 7 K expressed sequence tags (EST) microarray containing c. 5400 unique gene models. Moreover, z3HAC primed the release of terpene volatiles. * The widespread priming response suggests an adaptive benefit to detecting z3HAC as a wound signal. Thus, woody plants can detect and use z3HAC as a signal to prime defenses before actually experiencing damage. GLVs may therefore have important ecological functions in arboreal ecosystems.

Proteomic analysis of the cambial region in juvenileEucalyptus grandis at three ages

Recent advances in genomics and proteomics have provided an excellent opportunity to understand complex biological processes such as wood formation at the gene and protein levels. The aim of this work was to describe the proteins participating in the processes involved in juvenile wood formation by isolating proteins from the cambial region of Eucalyptus grandis, at three ages of growth (6-month-old seedlings, 3- and 6-year-old trees), and also to identify proteins differentially expressed. Using a 2-D-LC-MS/MS strategy we identified a total of 240 proteins, with 54 corresponding spots being present in at least two ages. Overall, nine proteins classified into the functional categories of metabolism, cellular processes, and macromolecular metabolism showed significant changes in expression. Proteins were classified into seven main functional categories, with metabolism representing 35.2% of the total proteins identified. The comparison of the reference maps showed not only differences in the expression pattern of individual proteins at each age, but also among isoforms. The results described in this paper provide a dynamic view of the proteins involved in the formation of juvenile wood in E. grandis.

Treatment of chickpea with Rhizobium isolates enhances the expression of phenylpropanoid defense-related genes in response to infection by Fusarium oxysporum f. sp. ciceris

Differential expression of phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS) and isoflavone reductase (IFR) genes involved in phenylpropanoids metabolism was investigated using Northern blot analyses in chickpea seedlings bacterized with Rhizobium isolates (PchDMS and Pch43) and further challenged with Fusarium oxysporum f. sp. ciceris (Foc) race 0. Gene activation patterns in the moderately resistant accession INRAT87/1 were compared with those exhibited by the susceptible accession ILC482 at various time intervals after inoculation with Foc, to determine whether differences in levels or timing of transcript accumulation could be correlated with differences in the susceptibility of chickpea accessions to Foc. Gene activation was higher in the moderately resistant accession INRAT87/1 than in the susceptible ILC482. Pre-treatment of chickpea seedlings with Rhizobium isolates before inoculation with the pathogen enhanced the accumulation of the three genes' mRNA transcripts. In parallel, changes in the soluble phenolic pool produced through pathways involving these enzymes were analyzed in chickpea roots. A strong accumulation of these compounds was revealed at 72 hpi in both accessions. After that time, these high levels of phenolic compounds were maintained until the end of the experiment in the moderately resistant accession, while they have significantly declined in the susceptible accession. HPLC analyses revealed a very high accumulation of the constitutive isoflavones, formononetin and biochanin A and their glycoside conjugates in chickpea roots inoculated with Rhizobium isolates and/or challenged with Foc, as compared to the controls. Our results suggest that the increased accumulation of phenolic compounds, observed in chickpea seedlings inoculated with Foc, can be attributed to increased expression of genes in the phenylpropanoid pathway and that such gene expression is enhanced by pre-treatment with Rhizobium isolates.

Genome-wide analyses of the structural gene families involved in the legume-specific 5-deoxyisoflavonoid biosynthesis of Lotus japonicus

A model legume Lotus japonicus (Regel) K. Larsen is one of the subjects of genome sequencing and functional genomics programs. In the course of targeted approaches to the legume genomics, we analyzed the genes encoding enzymes involved in the biosynthesis of the legume-specific 5-deoxyisoflavonoid of L. japonicus, which produces isoflavan phytoalexins on elicitor treatment. The paralogous biosynthetic genes were assigned as comprehensively as possible by biochemical experiments, similarity searches, comparison of the gene structures, and phylogenetic analyses. Among the 10 biosynthetic genes investigated, six comprise multigene families, and in many cases they form gene clusters in the chromosomes. Semi-quantitative reverse transcriptase–PCR analyses showed coordinate up-regulation of most of the genes during phytoalexin induction and complex accumulation patterns of the transcripts in different organs. Some paralogous genes exhibited similar expression specificities, suggesting their genetic redundancy. The molecular evolution of the biosynthetic genes is discussed. The results presented here provide reliable annotations of the genes and genetic markers for comparative and functional genomics of leguminous plants.

Mutational analysis of NADH-binding residues in triphenylmethane reductase from Citrobacter sp. strain KCTC 18061P

Triphenylmethane reductase (TMR) catalyzes the NADH-dependent reduction of triphenylmethane dyes. Sequence alignment revealed a region with a conserved GXXGXXG motif near its N-terminus, which corresponds to a conserved structural motif of known dinucleotide-binding proteins. To verify whether some of these glycine residues are important for the enzyme catalysis, these three glycine residues (Gly-7, Gly-10 and Gly-13) were individually replaced by alanine using site-directed mutagenesis. The secondary structures of these mutants, as measured by circular dichroism spectroscopy, did not show remarkable differences as compared with the wild type. The V(max)/K(m) values of mutants G7A and G13A for both Basic fuchsin and NADH were increased about three and twofold over that of the wild type, respectively, whereas the V(max)/K(m) value of mutant G10A were decreased about sixfold. These results suggest that these three glycine residues are involved in the interaction with both substrate and cofactor for the catalytic activity of TMR.

Crystal structure of vestitone reductase from alfalfa (Medicago sativa L.)

Isoflavonoids are commonly found in leguminous plants, where they play important roles in plant defense and have significant health benefits for animals and humans. Vestitone reductase catalyzes a stereospecific NADPH-dependent reduction of (3R)-vestitone in the biosynthesis of the antimicrobial isoflavonoid phytoalexin medicarpin. The crystal structure of alfalfa (Medicago sativa L.) vestitone reductase has been determined at 1.4 A resolution. The structure contains a classic Rossmann fold domain in the N terminus and a small C-terminal domain. Sequence and structural analysis showed that vestitone reductase is a member of the short-chain dehydrogenase/reductase (SDR) superfamily despite the low levels of sequence identity, and the prominent structural differences from other SDR enzymes with known structures. The putative binding sites for the co-factor NADPH and the substrate (3R)-vestitone were defined and located in a large cleft formed between the N and C-terminal domains of enzyme. Potential key residues for enzyme activity were also identified, including the catalytic triad Ser129-Tyr164-Lys168. A molecular docking study showed that (3R)-vestitone, but not the (3S) isomer, forms favored interactions with the co-factor and catalytic triad, thus providing an explanation for the enzyme's strict substrate stereo-specificity.

Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.)

Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.