A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L.

Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein-Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.

WRKY transcription factors: evolution, regulation, and functional diversity in plants.

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

Molecular dissection of genes and promoters involved in glycyrrhizin biosynthesis revealed phytohormone induced modulation in Glycyrrhiza glabra L.

The study reports cloning and characterization of complete biosynthetic gene cluster committed to glycyrrhizin biosynthesis along with their corresponding promoter regions from Glycyrrhiza glabra. The identified genes namely, ß-amyrin synthase, ß-amyrin-11-oxidase, 11-oxo-beta-amyrin 30-oxidase and UDP-dependent glucosyltransferase, were hetrologously expressed in Nicotiana benthamiana for functional validation. The phyto-hormone, naphthalene acetic acid was shown to prompt maximum up regulation (1.3-14.0 folds) of all the genes, followed by gibberellic acid (0.001-10.0 folds) and abscisic acid (0.2-7.7 folds) treatments. The promoter-GUS fusion constructs infiltrated leaves of the identified genes exhibited enhanced promoter activity of ß-amyrin synthase (3.9 & 3.0 folds) and 11-oxo-beta-amyrin 30-oxidase (3.6 & 3.2 folds) under the GA3 and NAA treatments, respectively as compared to their respective untreated controls. The transcriptional control of the three phytohormones studied could be correlated to the cis-responsive elements present in the upstream regions of the individual genes. The study provided an insight into the intricate interaction between hormone-responsive motifs with the corresponding co-expression of the glycyrrhizin biosynthetic pathway genes. The study will help in understanding the phytohormones-mediated regulation of glycyrrhizin biosynthesis and its modulation in the plant.

Transcriptome-wide identification of squalene epoxidase genes from Glycyrrhiza glabra L.: expression analysis and heterologous expression of GgSQE1 suggest important role in terpenoid biosynthesis.

Squalene epoxidase (SQE) is a crucial regulatory enzyme for the biosynthesis of several important classes of compounds including sterols and triterpenoids. The present paper identified and characterised five SQE genes (GgSQE1 to GgSQE5) from Glycyrrhiza glabra through transcriptome data mining and homology-based cloning, for the first time. The phylogenetic analysis implied their functional divergence. The ORF corresponding to one of the five SQEs, namely, GgSQE1, was cloned and studied for its function in a heterologous system, following transient and stable expressions. The transient expression followed by GgSQE1 encoding protein purification suggested approximately 58.0-kDa protein following the predicted molecular mass of the deduced protein. The gene expression profiling based on qRT-PCR indicated its highest expression (6.4-folds) in the 10-month-old roots. Furthermore, ABA (12.4-folds) and GA3 (2.47) treatments upregulated the expression of GgSQE1 in the shoots after 10 and 12 hours, respectively, which was also reflected in glycyrrhizin accumulation. The inductive effects of ABA and GA3 over GgSQE1 expression were also confirmed through functional analysis of GgSQE1 promoters using GUS fusion construct. Stable constitutive expression of GgSQE1 in Nicotiana tabacum modulated the sterol contents. The study could pave the way for understanding the metabolic flux regulation concerning biosynthesis of related sterols and triterpenoids.

A Comprehensive Transcriptome-Wide Identification and Screening of WRKY Gene Family Engaged in Abiotic Stress in Glycyrrhiza glabra.

The study reports 147 full-length WRKY genes based on the transcriptome analysis of Glycyrrhiza genus (G. glabra and G. uralensis). Additional motifs in G. glabra included DivIVA (GgWRKY20) and SerS Superfamily (GgWRKY21) at the C-terminal, and Coat family motifs (GgWRKY55) at the N-terminal of the proteins, while Exo70 exo cyst complex subunit of 338 amino acid (GuWRKY9) was present at the N-terminal of G. uralensis only. Plant Zn cluster super-family domain (17 WRKYs) and bZIP domain (2 WRKYs) were common between the two species. Based on the number of WRKY domains, sequence alignment and phylogenesis, the study identified GuWRKY27 comprising of 3 WRKY domains in G. uralensis and a new subgroup-IIf (10 members), having novel zinc finger pattern (C-X4-C-X22-HXH) in G. glabra. Multiple WRKY binding domains (1-11) were identified in the promoter regions of the GgWRKY genes indicating strong interacting network between the WRKY proteins. Tissue-specific expression of 25 GgWRKYs, under normal and treated conditions, revealed 11 of the 18 induction factor triggered response corroborating to response observed in AtWRKYs. The study identified auxin-responsive GgWRKY 55 & GgWRKY38; GA3 responsive GgWRKYs15&59 in roots and GgWRKYs8, 20, 38, 57 &58 in the shoots of the treated plant. GgWRKYs induced under various stresses included GgWRKY33 (cold), GgWRKY4 (senescence), GgWRKYs2, 28 & 33 (salinity) and GgWRKY40 (wounding). Overall, 23 GgWRKYs responded to abiotic stress, and 17 WRKYs were induced by hormonal signals. Of them 13 WRKYs responded to both suggesting inter-connection between hormone signalling and stress response. The present study will help in understanding the transcriptional reprogramming, protein-protein interaction and cross-regulation during stress and other physiological processes in the plant.

Community structure, spatial distribution, diversity and functional characterization of culturable endophytic fungi associated with Glycyrrhiza glabra L.

A total of 266 endophytic fungal isolates were recovered from 1019 tissue segments of Glycyrrhiza glabra collected from four different locations in the North-Western Himalayas. The endophytes grouped into 21 genera and 38 different taxa. The host had strong affinity for the genus Phoma, followed by Fusarium. The species richness was highest at the sub-tropical location, followed by the sub-temperate location and the temperate locations, respectively. The tissue specificity of endophytes was also evident. Some endophytes showed potential antimicrobial activity against phyto-pathogens indicating that they may be helpful to the host in evading pathogens. All the endophytic taxa produced the plant growth promoting hormone, indole acetic acid (IAA), though in varying concentrations. None of these endophytes caused any symptoms of disease in co-cultivation with the tissue cultured plants. Further, all the endophytes had a positive influence on the phenolic and flavonoid content of the host. Three endophytes, Stagonosporopsis cucurbitacearum, Bionectria sp. and Aspergillus terreus also increased the host root (rhizome) and shoot growth visibly. Such endophytes are potential candidates for developing endophyte-based technologies for sustainable cultivation and enhanced productivity of G. glabra. This is the first report of community structure and biological properties of fungal endophytes associated with G. glabra.

Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing.

microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants.

Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

Isolation, Chemical Fingerprinting and Simultaneous Quantification of Four Compounds from Tanacetum gracile Using a Validated HPLC-ESI-QTOF-Mass Spectrometry Method.

The present study was conducted to carry out the phytochemical investigation of Tanacetum gracile Hook. f. & Thomson and to develop a method for the simultaneous quantification of the isolated compounds in the extracts ofT. gracile growing in different locations. Cluster analysis rectangular similarity matrix was performed to understand the chemical fingerprinting variations in the extracts. High-performance liquid chromatography-electrospray ionization-quadrupole-time-of-flight-mass spectrometry (HPLC-ESI-QTOF-MS) was used to quantify four bioactive compounds, and separation of the compounds was achieved on a reverse-phase C8 column using a mobile phase of acetonitrile: 0.1% formic acid in water with a gradient elution by maintaining the flow rate of 300 µL/min. The QTOF-MS was operated using the electro-spray ionization technique with the positive ion polarity mode. The calibration curves of four marker compounds were linear over the concentration range of 3.12-100 ng/µL (R(2)> 0.996). A specific, accurate and precise HPLC-ESI-QTOF-MS method was optimized for the determination of kaempferol, ketoplenolide, tetramethoxyflavone and artemetin both individually and simultaneously. Quantification of these chemical markers in different extracts was carried out using this validated method. Kaempferol was isolated for the first time from T. gracile.

Terpenoid and flavonoid spectrum of in vitro cultures of Glycyrrhiza glabra revealed high chemical heterogeneity: platform to understand biosynthesis.

Simultaneous qualitative and quantitative assessment of eight flavonoids and two terpenoids were performed in fourteen in vitro raised morphogenic cultures of Glycyrrhiza glabra. Our study revealed that the spectrum and production of ten compounds, under investigation, were higher in organized tissue than the undifferentiated mass, however, aerial portions of the in vitro raised plants (leaf and stem) were found to be devoid of therapeutically relevant triterpenoid, glycyrrhizin. A correlation was observed between cell maturation, morphological differentiation and glycyrrhizin accumulation. Mature stolons (4 months) were characterized by the maximum accumulation of glycyrrhizin (8.60 µg/mg) in in vitro plantlets. The cytotoxic effect of the extracts evaluated against a panel of human cancer cell lines (in vitro) indicated that the pancreatic cell line (MIA-PaCa-2) were sensitive to all the fourteen extracts investigated. To the best of our knowledge this is the first comprehensive report relating plant growth regulators to metabolite spectrum and cytotoxic assessment in in vitro raised G. glabra cultures. Overall, our findings demonstrated that the metabolite spectrum of in vitro raised morphogenetic lines, under different stages of maturation, might offer a platform to understand the regulatory aspects of the concerned metabolite pathway and their consequent role in differentiation.

Multi-elemental profiling and chemo-metric validation revealed nutritional qualities of Zingiber officinale.

Ginger rhizome is a valued food, spice and an important ingredient of traditional systems of medicine of India, China and Japan. An Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) based multi-elemental profiling was performed to assess the quantitative complement of elements, nutritional quality and toxicity of 46 ginger germplasms, collected from the north western Himalayan India. The abundance of eighteen elements quantified in the acid digested rhizomes was observed to be K>Mg>Fe>Ca>Na>Mn>Zn>Ba>Cu>Cr>Ni>Pb>Co>Se>As>Be>Cd. Toxic element, Hg was not detected in any of the investigated samples. Chemometric analyses showed positive correlation among most of the elements. No negative correlation was observed in any of the metals under investigation. UPGMA based clustering analysis of the quantitative data grouped all the 46 samples into three major clusters, displaying 88% similarity in their metal composition, while eighteen metals investigated grouped into two major clusters. Quantitatively, all the elements analyzed were below the permissible limits laid down by World Health Organization. The results were further validated by cluster analysis (CA) and principal component analysis (PCA) to understand the ionome of the ginger rhizome. The study suggested raw ginger to be a good source of beneficial elements/minerals like Mg, Ca, Mn, Fe, Cu and Zn and will provide platform for understanding the functional and physiological status of ginger rhizome.

Direct rhizogenesis, in vitro stolon proliferation and high-throughput regeneration of plantlets in Glycyrrhiza glabra.

Direct rhizogenesis from leaf explants and establishment of an in vitro stolon culture system and subsequent plant regeneration for Glycyrrhiza glabra have been described. MS liquid medium supplemented with 0.01 mg l-1 of NAA was most effective for stolon proliferation. Extensive proliferation of stolon and shoot regeneration was achieved on medium containing 3 % sucrose with 0.01 mg l-1 NAA. Stolons with nodes showing growth was transferred under light for plantlet regeneration in the same medium. This paper is the first report in G. glabra describing a complete regeneration procedure via in vitro stolon proliferation along with quantitative data for glycyrrhizin and genetic fidelity of plant regenerated in vitro there from. In vitro stolon proliferation described here would be an efficient way for regeneration of plants for functional genomics studies and better understanding of glycyrrhizin (GA) metabolism.

Chromolithic method development, validation and system suitability analysis of ultra-sound assisted extraction of glycyrrhizic acid and glycyrrhetinic acid from Glycyrrhiza glabra.

An ultrasound-assisted extraction and chromolithic LC method was developed for simultaneous determination of glycyrrhizic acid (GA) and glycyrrhetinic acid (GL) from the root extract of Glycyrrhizza glabra using RPLC-PDA. The developed method was validated according to the International Conference on Harmonisation. The method exhibited good linearity (r2 > 0.9989) with high precision and achieved good accuracies between 97.5 to 101.3% of quantitative results. The method is more sensitive and faster (resolved within ten minutes) than the earlier developed methods using normal LC columns.

A comprehensive analysis of fifteen genes of steviol glycosides biosynthesis pathway in Stevia rebaudiana (Bertoni).

Stevia [Stevia rebuaidana (Bertoni); family: Asteraceae] is known to yield diterpenoid steviol glycosides (SGs), which are about 300 times sweeter than sugar. The present work analyzed the expression of various genes of the SGs biosynthesis pathway in different organs of the plant in relation to the SGs content. Of the various genes of the pathway, SrDXS, SrDXR, SrCPPS, SrKS, SrKO and three glucosyltransferases namely SrUGT85C2, SrUGT74G1 and SrUGT76G1 were reported from stevia. Here, we report cloning of seven additional full-length cDNA sequences namely, SrMCT, SrCMK, SrMDS, SrHDS, SrHDR, SrIDI and SrGGDPS followed by expression analysis of all the fifteen genes vis-à-vis SGs content analysis. SGs content was highest in the leaf at 3rd node position (node position with reference to the apical leaf as the first leaf) as compared to the leaves at other node positions. Except for SrDXR and SrKO, gene expression was maximum in leaf at 1st node and minimum in leaf at 5th node. The expression of SrKO was highest in leaf at 3rd node while in case of SrDXR expression showed an increase up to 3rd leaf and decrease thereafter. SGs accumulated maximum in leaf tissue followed by stem and root, and similar was the pattern of expression of all the fifteen genes. The genes responded to the modulators of the terpenopids biosynthesis. Gibberellin (GA(3)) treatment up-regulated the expression of SrMCT, SrCMK, SrMDS and SrUGT74G1, whereas methyl jasmonate and kinetin treatment down-regulated the expression of all the fifteen genes of the pathway.

Composition of a monoterpenoid-rich essential oil from the rhizome of Zingiber officinale from north western Himalayas.

The chemical composition of the essential oil from the rhizome of ginger (Zingiber officinale Roscoe), collected from Nahan, Himachal Pradesh, India, was determined by gas chromatography and GC-MS. Fifty-one compounds, representing 95.1% of the oil, were identified. The oil was characterized by relatively large amounts of the monoterpenoids 1,8-cineole (10.9%), linalool (4.8%), borneol (5.6%), alpha-terpineol (3.6%), neral (8.1%), geraniol (14.5%), geranial (9.5%), trans-dimethoxy citral (5.0%) and geranyl acetate (6.3%). Five compounds, namely trans-linalool oxide, trans-linalool oxide acetate, (Z)-dimethoxycitral, (E)-dimethoxy citral and epi-zingiberenol are reported for the first time in oil of ginger.

RP-thin layer chromatographic method for the quantification of three gingerol homologs of ultrasonic-assisted fresh rhizome extracts of Zingiber officinale collected from North Western Himalayas.

A rapid and sensitive RP high-performance thin-layer chromatographic (RP-HPTLC) methodology was developed and validated for the quantitative estimation of gingerols in methanolic extract of fresh ginger rhizome. The samples were chromatographed on RP-TLC glass plates pre-coated with RP-18 60F(254) as the stationary phase. Linear ascending development was carried out in twin trough glass chamber saturated with ternary-solvent system consisting of acetonitrile-water-formic acid (7:2:1 v/v/v) at room temperature (25+/-2 degrees C) and plates were scanned at 500 nm. The system was found to give compact spots for gingerols (R(f) values of 6-gingerol 0.73+/-0.04, 8-gingerol 0.59+/-0.08 and 10-gingerol 0.36+/-0.05). Linearity was found to be in the range of 140-840 ng/spot for 6-gingerol, 168-1008 ng/spot for 8-gingerol and 136-816 ng/spot for 10-gingerol with significantly high value of correlation coefficient. The linear regression analysis data for the calibration plots showed linear relationship (r(2)) and ranged from 0.9992 to 0.9937 for 6-, 8- and 10-gingerol. The method was used for routine analyses and to obtain relative amounts of the gingerols in the fresh rhizomes of the ginger cultivated in different locations of Uttarakhand and Himachal Pradesh of North Western Himalayas (India).