Chilling susceptibility in mungbean varieties is associated with their differentially expressed genes.

BACKGROUND: Mungbean (Vigna radiata L. Wilczek) is an economically important legume of high nutritional value, however, its cultivation is limited by susceptibility to chilling. Varieties NM94 and VC1973A, with differential susceptibility to stress, serve as good materials for uncovering how they differ in chilling tolerance. This study aimed to identify the ultrastructural, physiological and molecular changes to provide new insights on the differential susceptibility to chilling between varieties VC1973A and NM94. RESULTS: Chilling stress caused a greater reduction in relative growth rate, a more significant decrease in maximum photochemical efficiency of PSII and DPPH scavenging activity and more-pronounced ultrastructural changes in VC1973A than in NM94 seedlings. Comparative analyses of transcriptional profiles in NM94 and VC1973A revealed that the higher expression of chilling regulated genes (CORs) in NM94. The transcript levels of lipid transfer protein (LTP), dehydrin (DHN) and plant defensin (PDF) in NM94 seedlings after 72 h at 4 °C was higher than that in its parental lines VC1973A, 6601 and VC2768A. CONCLUSIONS: Our results suggested that LTP, DHN and PDF may mediate chilling tolerance in NM94 seedlings.

Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes.

DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes.

Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.

The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1) encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+)-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC)/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+)-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.

Cold response in Phalaenopsis aphrodite and characterization of PaCBF1 and PaICE1.

Phalaenopsis is a winter-blooming orchid genus commonly cultivated in tropical Asian countries. Because orchids are one of the most economically important flower crops in Taiwan, it is crucial to understand their response to cold and other abiotic stresses. The present study focused on gene regulation of P. aphrodite in response to abiotic stress, mainly cold. Our results demonstrate that P. aphrodite is sensitive to low temperatures, especially in its reproductive stage. We found that after exposure to 4°C, plants in the vegetative stage maintained better membrane integrity and photosynthetic capacity than in the flowering stage. At the molecular level, C-repeat binding factor1 (PaCBF1) and its putative target gene dehydrin1 (PaDHN1) mRNAs were induced by cold, whereas inducer of CBF expression1 (PaICE1) mRNA was constitutively expressed. PaICE1 transactivated MYC motifs in the PaCBF1 promoter, indicating that up-regulation of PaCBF1 may be mediated by the binding of PaICE1 to MYC motifs. Overexpression of PaCBF1 in transgenic Arabidopsis induced AtCOR6.6 and RD29a without cold stimulus and maintained better membrane integrity after cold stress. Herein, we present evidence that cold induction of PaCBF1 transcripts in P. aphrodite may be transactivated by PaICE1 and consequently protect plants from cold damage through up-regulation of cold-regulated (COR) genes, such as DHN. To our knowledge, this study is the first report of the isolation and characterization of CBF, DHN and ICE genes in the Orchidaceae family.

Putative genes involved in saikosaponin biosynthesis in Bupleurum species.

Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species is summarized, followed by discussions on identification and characterization of genes involved in the biosynthesis of saikosaponins. The purpose is to provide a brief review of gene extraction, functional characterization of isolated genes and assessment of expression patterns of genes encoding enzymes in the process of saikosaponin production in Bupleurum species, mainly B. kaoi. We focus on the effects of MeJA on saikosaponin production, transcription patterns of genes involved in biosynthesis and on functional depiction.

Arabidopsis ENDO2: its catalytic role and requirement of N-glycosylation for function.

The Arabidopsis thaliana At1g68290 gene encoding an endonuclease was isolated and designated ENDO2, which was cloned into a binary vector to overexpress ENDO2 with a C-terminal 6 × His-tag in A. thaliana. Our Arabidopsis transgenic lines harboring 35SP::ENDO2 produced stable active enzyme with high yield. The protein was affinity purified from transgenic plants, and its identity was confirmed by liquid chromatography-mass spectrometry and automatic Edman degradation. ENDO2 enzyme digests RNA, ssDNA, and dsDNA, with a substrate preference for ssDNA and RNA. The activity toward ssDNA (361.7 U/mg) is greater than its dsDNase activity (14.1 U/mg) at neutral pH. ENDO2 effectively cleaves mismatch regions in heteroduplex DNA containing single base pair mismatches or insertion/deletion bases and can be applied to high-throughput detection of single base mutation. Our data also validated that the removal of sugar groups from ENDO2 strongly affects its enzymatic stability and activity.

Characterization of a novel Y2K-type dehydrin VrDhn1 from Vigna radiata.

A novel dehydrin gene (VrDhn1) was isolated from an embryo cDNA library of Vigna radiata (L.) Wilczek (mungbean) variety VC1973A. The intronless VrDhn1 gene encodes a protein belonging to the Y(2)K-type dehydrin family. VrDhn1 protein accumulated in embryos and cotyledons during seed maturation and disappeared 2 days after seed imbibition (DAI). The expression of VrDhn1 mRNA and accumulation of VrDhn1 protein were at high levels in mature seeds, but neither mRNA nor protein was detected in mungbean vegetative tissues under normal growth conditions. The VrDhn1 mRNA level was extremely high in mature seeds and decreased to ∼30% at 1 DAI, and was not detectable at ~7 DAI. Tissue dehydration, salinity and exogenous ABA markedly induced VrDhn1 transcripts in plants as measured by quantitative real-time reverse transcription-PCR (qRT-PCR). VrDhn1 protein was not detected using immunoblots in seedlings under stress treatments. In mature seeds or 1 DAI seedlings, VrDhn1 proteins were immunolocalized in the nucleus and cytoplasm. VrDhn1 exhibited low affinity for non-specific interaction with DNA using electrophoretic mobility shift assays (EMSAs), and the exogenous addition of Zn(2+) or Ni(2+) stimulated interaction. The His-tagged VrDhn1 (30.17 kDa) protein showed a molecular mass of 63.1 kDa on gel filtration, suggesting a dimer form. This is the first report showing that a Y(2)K-type VrDhn1 enters the nucleus and interacts with DNA during seed maturation.

Changes in the endopolyploidy pattern of different tissues in diploid and tetraploid Phalaenopsis aphrodite subsp. formosana (Orchidaceae).

Endopolyploidy is frequently observed during development in plant species. Patterns of endopolyploidy are diverse in the various organs of different plant species. However, little is known about the role of endopolyploidization and its significance in orchids. This study was undertaken to determine the extent of endopolyploidy in different tissues of the diploid and tetraploid genotypes of Phalaenopsis aphrodite subsp. formosana and to examine the factors that contribute to increased ploidy levels. Endopolyploidy occurs in various tissues of diploid and tetraploid orchids, at different developmental stages and under different culture conditions, as determined by flow cytometry. In this study, different patterns of endopolyploidy were observed in parts of the protocorms, leaves, roots and flowers. Endopolyploidy was found in all tissues studied except the pollinia and the tetraploid ovaries. A higher degree of endopolyploidy was observed in mature tissues compared to young tissues, greenhouse-grown plants compared to in vitro plants and diploid plants compared to tetraploid plants. We discuss the relationships between endopolyploidization and several factors related to plant growth, as well as some practical considerations of these findings.

Functional characterization of three ethylene response factor genes from Bupleurum kaoi indicates that BkERFs mediate resistance to Botrytis cinerea.

Three novel ethylene response factor (ERF) genes, BkERF1, BkERF2.1 and BkERF2.2, were isolated from a medicinal plant, Bupleurum kaoi. The deduced BkERFs contain a canonical nuclear localization signal and an ERF/AP2 DNA binding domain. RNA gel blot analysis revealed that BkERF1 and BkERF2.1 were ubiquitously expressed at low levels in all parts of mature plants, and that BkERF2.2 was expressed at moderate levels in vegetative tissues. Exogenous application of methyl jasmonate induced BkERF1/2.1/2.2 transcripts. BkERF2.2 transcript levels were slightly increased by addition of ethephon and salicylic acid. BkERFs were localized in the plant nucleus and functioned as transcriptional activators. In B. kaoi cells overexpressing BKERFs, inoculation with Botrytis cinerea increased expression of some defense genes which are associated with enhanced disease resistance. Similarly, overexpression of BkERFs in transgenic Arabidopsis thaliana resulted in elevated mRNA levels of the defense gene PDF1.2, and in enhanced resistance to B. cinerea. Collectively, these results provide evidence that BkERFs mediate the expression of defense-related genes in plants.

Characterization of the Scutellaria barbata glycosyltransferase gene and its promoter.

The conversion of flavonoid aglycones to their glycosides by plant glycosyltransferases may affect a wide range of outcomes, including stability, solubility and bioavailability. Scutellaria barbata, rich in flavonoid glycosides, is widely used as a traditional Chinese herbal medicine. In this study, a flavonoid glycosyltransferase cDNA (SbUGT) and its promoter from S. barbata were cloned and characterized as a flavonoid glycosyltransferase using whole-cell biotransformation. Fragments of different lengths of the 5'-flanking region of the SbUGT gene were fused to the beta-glucuronidase (GUS) gene and analyzed with transgenic Arabidopsis plants using histochemical and fluorometric assays. GUS activity in transgenic plants carrying the SbP-850U construct (-850 to +86 relative to the transcription start site) displayed the highest level and was enhanced by salt and methyl jasmonate, similar to the expression patterns of the endogenous SbUGT. GUS activity disappeared when the promoter was deleted to -98, and deletion analyses indicated the existence of positive and negative regulatory element(s). Unexpectedly, plants carrying the construct SbP-102U (-102 to +86) exhibited strong GUS activity exclusively in the roots. Our experiments revealed that the specific expression is mediated by different promoter regions and the unique region driving root-preferred expression can be used as a root-specific promoter.

Rapid authentication of Bupleurum species using an array of immobilized sequence-specific oligonucleotide probes.

Standardization and modernization of Chinese medicinal herbs are limited partially by misidentification of processed materials. Our goal was to develop an efficient method for verification of Chinese medicinal herbs, based on the variable sites of the rDNA internal transcribed spacer (ITS) region. We analyzed sequence differences in ITS of three Bupleurum species, B. kaoi Liu Chao et Chuang, B. falcatum L. and B. chinense DC., and developed a rapid detection method using a sequence-specific oligonucleotide probe (SSOP) array. The SSOP array, composed of poly-T tailed sequence-specific oligonucleotides, was hybridized to the digoxigenin (DIG)-labeled target ITS DNA of the Bupleurum species. The detected signals corresponded precisely to the specific sequences. This array provides a reliable and economical method for authenticating a large number of Chinese medicinal herbs. The short duration of the procedure (within 30 h) makes it an especially useful tool in verifying processed plant material.

Depsipeptide (FK228) inhibits growth of human prostate cancer cells.

FK228 (depsipeptide) is a natural prodrug that inhibits class I histone deacetylases. We aimed to investigate the effects FK228 has on prostate cancer cells in vivo. In non-obese diabetic-severe combined immunodeficient mice implanted with human prostate cancer cells, 50 mg/kg FK228 given orally 3 times a week inhibited tumor growth and metastasis. The median time to the experimental end point (tumor volume 2 cm(3) or death) in the untreated group was 52 days, and average tumor volume was 0.8 +/- 0.18 cm(3). At the same time, 94.4% of FK228-treated mice survived and had average tumor volumes of 0.37 +/- 0.1 cm(3). All untreated animals died at 98 days, whereas, 61% of treated animal remained alive. Sizeable metastatic tumors positively stained for prostate-specific antigen (PSA), and limited air gaps were found in the lungs of untreated mice. In animals treated with FK228, lung morphology appeared normal. Primary tumors of treated animals were highly positive for PSA, and had an increased level of p21 and the proapoptotic protein Bax. Sections taken from FK228-treated animals and examined under an electron microscope showed condensed chromatin and apoptotic bodies. PSA serum levels were higher in untreated than in treated animals and correlated with tumor volume. Because prolonged oral administration of 50 mg/kg or a single oral dose of 1.2 g/kg FK228 did not cause adverse effects and inhibited proliferation of human prostate cancer cells in vivo, FK228 likely has a potential anticancer effect for prostate cancer.

Early developmental and stress responsive ESTs from mungbean, Vigna radiata (L.) Wilczek, seedlings.

Although mungbean (Vigna radiata (L.) Wilczek) is commonly used as human food; the genomic resources of this species available in databases are limited. This study aims to develop expressed sequence tag (EST) resources for mungbean genes informative to early seedling development and chilling response. Two mungbean varieties that differ in disease resistance were found to also differ in their susceptibility to chilling temperatures. A total of 1,198 ESTs were obtained from one cDNA library and four PCR-select cDNA subtraction libraries; among these 523 were clustered into 136 contigs and 675 were singletons. The 811 non-redundant uniESTs were compared to GenBank using the Basic Local Alignment Search Tool (BLAST) and WU-BLAST algorithms, of these only 489 uniESTs had significant sequence homology, which may be involved in resuming the metabolic activity of seedlings, switching on photomorphogenesis, fuelling photosynthesis and/or initiating the unique developmental programs. Their encoded proteins may associate with regulatory proteins to trigger a direct stress response or participate in acclimation to environmental stressors. The uniEST platform reported will enrich the genomic resources of mungbean for functional genomic research on seedling development and chilling response of tropical crops and provide targets for improving the chilling tolerance of the tropical crops.

Authentication of medicinal herbs using PCR-amplified ITS2 with specific primers.

Different parts of medicinal herbs have long been used as traditional Chinese drugs for treating many diseases, whereas materials of similar morphology and chemical fingerprints are often misidentified. Analyses of sequence variations in the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) have become a valid method for authentication of medicinal herbs at the intergenic and interspecific levels. DNA extracted from processed materials is usually severely degraded or contaminated by microorganisms, thus generates no or unexpected PCR products. The goal of this study is to apply the ITS fragments selectively amplified with two designed primer sets for efficient and precise authentication of medicinal herbs. The designed primers led to an accurate PCR product of the specific region in ITS2, which was confirmed with DNA extracted from 55 processed medicinal herbs belonging to 48 families. Moreover, the selectively amplified ITS2 authenticated five sets of easily confusable Chinese herbal materials. The designed primers were proven to be suitable for a broad application in the authentication of herbal materials.

Developmental expression of three mungbean Hsc70s and substrate-binding specificity of the encoded proteins.

We isolated three mungbean Hsc70 cDNAs (VrHsc70-1, 70-2 and 70-3) and characterized their developmental expression at both the transcript and protein levels. We also characterized the binding specificity between each VrHsc70 protein and its potential substrates. RNase protection assays showed that these three cytosolic VrHsc70 genes were expressed similarly in all organs at all times during the mungbean life cycle, except at the initiation of germination and during late seed embryogenesis. Western blotting analyses showed that a different group of cytosolic VrHsc70 proteins accumulated in dehydrated seeds during seed maturation and the accumulated proteins remained high during the early stages of germination. Binding specificities of these three mungbean Hsc70s were determined using the C-terminal 30 kDa of the three VrHsc70s to select bound heptapeptides using phage display screening, and were confirmed by ELISA. We found that the heptapeptides, KVWVLPI, KLWVIPQ and YAPLSRL, specifically bound to the C-terminal 30 kDa region of VrHsc70-1, 70-2 and 70-3, respectively. The hydrophobic residues in the core of the heptapeptides, as well as residues 6 and 7, might contribute to the binding specificity. Our results indicate that the function of these three VrHsc70s may not be important in seed maturation or in desiccation tolerance, but are more likely involved in normal growth and development.

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.

MOTIVATION: Genome-wide gene expression programs have been monitored and analyzed in the yeast Saccharomyces cerevisiae, but how cells regulate global gene expression programs in response to environmental changes is still far from being understood. We present a systematic approach to quantitatively characterize the transcriptional regulatory network of the yeast cell cycle. For the interpretative purpose, 20 target genes were selected because their expression patterns fluctuated in a periodic manner concurrent with the cell cycle and peaked at different phases. In addition to the most significant five possible regulators of each specific target gene, the expression pattern of each target gene affected by synergy of the regulators during the cell cycle was characterized. Our first step includes modeling the dynamics of gene expression and extracting the transcription rate from a time-course microarray data. The second step embraces finding the regulators that possess a high correlation with the transcription rate of the target gene, and quantifying the regulatory abilities of the identified regulators. RESULTS: Our network discerns not only the role of the activator or repressor for each specific regulator, but also the regulatory ability of the regulator to the transcription rate of the target gene. The highly coordinated regulatory network has identified a group of significant regulators responsible for the gene expression program through the cell cycle progress. This approach may be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes. SUPPLEMENTARY INFORMATION: Matlab code and test data are available at http://www.ee.nthu.edu.tw/~bschen/quantitative/regulatory_network.htm

Cloning and characterization of two novel lipid transfer protein I genes in Vigna radiata.

Two full-length lipid transfer protein (LTP) cDNAs were isolated from mungbean (Vigna radiata) and designated Vrltp1 and Vrltp2. The deduced amino acid sequences contain the two highly conserved pentapeptides characteristic of plant LTPIs suggesting these Vrltps belong to the LTPI gene family. Vrltp1 mRNA was detected in developing seeds, but Vrltp2 mRNA was not. Within the vegetative tissues, the Vrltp1 and Vrltp2 mRNAs were present only in leaves and stems, but not root tips. Salt and dehydration stresses and exogenous abscisic acid (ABA) treatments resulted in increased mRNA levels of both Vrltps in leaves. We suggest that these unique Vrltps are specific to growing shoot tissues, and may play an important role in plant acclimation to water stress.