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1.  Identity and pharmacognosy of Ruta graveolens Linn 
Ancient Science of Life  2012;32(1):16-19.
Ruta graveolens L., is a odoriferous herb belonging to the family Rutaceae. It is the source of Rue or Rue oil, called as Sadab or Satab in Hindi. It is distributed throughout the world and cultivated as a medicinal and ornamental herb. The ancient Greeks and Romans, held the plant in high esteem. It is used in Ayurveda, Homoeopathy and Unani. Phytochemical constituents and pharmacological properties were studied in depth. In 14 species of genus Ruta, R. graveolens and R. chalepensis are available in India and also cultivated in gardens. Taxonomical characters to identify the Indian plants are very clear with fringed and or non-fringed petals. However, references to it are confused in the traditional literature. Due to sharing of regional language name, its identity is confused with Euphorbia dracunculoides. Morphological and anatomical characters were described. Pharmacognostic studies with microscopic characters were also published. Upon reviewing the anatomical characters and pharmacognostic characters one finds that it is highly confused and conflicting. The characters described are opposite of each other and authenticity of the market sample of R. graveolens cannot be guaranteed and able to be differentiated from R. chalepensis. Present work is to describe the pharmacognostic characters of R. graveolens to differentiate it from R. chalepensis. It is concluded that morphologically, R. graveolens can be identified with its non-fringed petals and blunted apices of fruit lobes. Whereas, in R. chalepensis petals are fringed or ciliated and apices of the fruit lobes are sharp and projected. Microscopically, in stem of R. graveolens pericyclic fibers have wide lumen. Whereas, in R. chalepensis, it is narrow. The published pharmacognosy reports do not pertain to authentic plant or some of the characteristic features like glandular trichomes are not observed in our samples.
doi:10.4103/0257-7941.113792
PMCID: PMC3733200  PMID: 23929988
Pharmacognosy; ruta chalepensis; ruta graveolens; rutaceae
2.  Effects of Naturally Occurring Coumarins on Hepatic Drug Metabolizing Enzymes in Mice 
Toxicology and applied pharmacology  2008;232(2):337-350.
Cytochromes P450 (P450s) and glutathione S-transferases (GSTs) constitute two important enzyme families involved in carcinogen metabolism. Generally, P450s play activation or detoxifying roles while GSTs act primarily as detoxifying enzymes. We previously demonstrated that oral administration of the linear furanocoumarins, isopimpinellin and imperatorin, modulated P450 and GST activities in various tissues of mice. The purpose of the present study was to compare a broader range of naturally occurring coumarins (simple coumarins, and furanocoumarins of the linear and angular type) for their abilities to modulate hepatic drug metabolizing enzymes when administered orally to mice. We now report that all of the different coumarins tested (coumarin, limettin, auraptene, angelicin, bergamottin, imperatorin and isopimpinellin) induced hepatic GST activities, whereas the linear furanocoumarins possessed the greatest abilities to induce hepatic P450 activities, in particular P450 2B and 3A. In both cases, this corresponded to an increase in protein expression of the enzymes. Induction of P4502B10, 3A11, and 2C9 by xenobiotics often are a result of activation of the pregnane X receptor (PXR) and/or constitutive androstane receptor (CAR). Using a pregnane X receptor reporter system, our results demonstrated that isopimpinellin activated both PXR and its human ortholog SXR by recruiting coactivator SRC-1 in transfected cells. In CAR transfection assays, isopimpinellin counteracted the inhibitory effect of androstanol on full length mCAR, a Gal4-mCAR ligand binding domain fusion, and restored coactivator binding. Orally administered isopimpinellin induced hepatic mRNA expression of Cyp2b10,Cyp3a1, GSTa in CAR(+/+) wild-type mice. In contrast, the induction of Cyp2b10 mRNA by isopimpinellin was attenuated in the CAR(−/−) mice, suggesting that isopimpinellin induces Cyp2b10 via the CAR receptor. Overall, the current data indicate that naturally occurring coumarins have diverse activities in terms of inducing various xenobiotic metabolizing enzymes based on their chemical structure.
doi:10.1016/j.taap.2008.07.004
PMCID: PMC2585982  PMID: 18692084
coumarins; furanocoumarins; P450s; pregnane X-receptor; constitutive androstane receptor
3.  Effect of Ruta graveolens and Cannabis sativa alcoholic extract on spermatogenesis in the adult wistar male rats 
Objective:
The present study was undertaken to evaluate the effects of alcohol extracts of Ruta graveolens and Cannabis sativa that were used traditionally in medieval Persian medicine as male contraceptive drugs, on spermatogenesis in the adult male rats.
Materials and Methods:
Ethanol extracts of these plants were obtained by the maceration method. The male rats were injected intraperitionaly with C. sativa and R. graveolens 5% ethanol extracts at dose of 20 mg/day for 20 consecutive days, respectively. Twenty-four hours after the last treatment, testicular function was assessed by epididymal sperm count.
Result:
The statistical results showed that the ethanol extracts of these plants reduced the number of sperms significantly (P=0.00) in the treatment groups in comparison to the control group. The results also showed that the group, treated by extract of R. graveolens reduced spermatogenesis more than the group treated by extracts of C. sativa.
Conclusion:
The present study demonstrated the spermatogenesis reducing properties of the ethanol extracts of R. graveolens and C. sativa in the adult male wistar rats but more studies are necessary to reveal the mechanism of action that is involved in spermatogenesis.
doi:10.4103/0970-1591.33720
PMCID: PMC2721602  PMID: 19718326
Cannabis sativa; fertility-decreasing properties; Ruta graveolens; spermatogenesis
4.  Acute Effects of Ruta graveolens L. on Sperm Parameters and DNA Integrity in Rats 
Background
Increase in world population is one of the serious and threatening issues in this century. Therefore, it is vitally important to find safe and effective contraceptive methods, especially for men which already have few choices in this regard. Medicinal plants that were used for contraception in ancient times could be good sources of investigation in this filed. Ruta graveolens L. is one the plants introduced in the Iranian traditional medicine as an oral male contraception to be used before intercourse. In this study we tried to investigate the probable effects of the plant on the spermatozoa of male rats.
Methods
Ruta graveolens L. aqueous extract (5 g/kg) was administered orally to five groups of male rats and sperm motility was checked after half, one, two, four and six hours later. Moreover, one group of rats served as the control group. Subsequently, viability of cells (Eosin-Nigrosin staining), morphological changes (Diff-Quick staining), DNA status (acridine orange dye) and serum testosterone levels were assessed in the treated groups which had significant immotile spermatozoa. For statistical analysis, Student's t-test and one-way ANOVA with Tukey's post-hoc test were employed for comparison between groups.
Results
A significant reduction in sperm motility was seen one hour after administration of the extract in the case groups compared to the controls (36% vs. 68.15%, respectively, p <0.01). The motility gradually increased afterwards, and by 6 hours, it was the same as the control group (65.43% and 68.15%, respectively). No significant changes were seen in viability, morphology or DNA structure of spermatozoa in each group. Testosterone levels did not show any significant changes in the treated groups when compared with the controls.
Conclusion
Since a significant temporary immobility of spermatozoa without any adverse effects on other sperm characteristics occurred upon the administration of Ruta graveolens L. aqueous extract, it seems that this plant might have the potential to be used for the suggested male contraception.
PMCID: PMC3719372  PMID: 23926522
Male contraception; Rat; Ruta graveolens L.; Sperm function assay; Spermatozoa; Iranian traditional medicine
5.  Ruta Graveolens Extract Induces DNA Damage Pathways and Blocks Akt Activation to Inhibit Cancer Cell Proliferation and Survival 
Anticancer research  2011;31(1):233-241.
Background
Ruta graveolens is a medicinal herb that has been used for centuries against various ailments. This study examined the anticancer properties of the herb using cancer cell lines.
Materials and Methods
Methanolic extract of R. graveolens was tested on colon, breast and prostate cancer cells. Viability, cell cycle profiles, clonogenicity and capase activation were measured. Induction and subcellular localizations of p53, 53BP1 and γ-H2AX proteins were examined.
Results
the extract dose-dependently decreased the viability and the clonogenicity of treated cells and induced G2/M arrest, aberrant mitoses, and caspase-3 activation. It also induced the p53 pathway and focal concentration of the DNA damage response proteins 53BP1 and γ-H2AX. Moreover, the levels of phospho-Akt and cyclin B1 were reduced by treatment, whereas only cyclin B1 was reduced in normal dermal fibroblasts.
Conclusion
R. graveolens extract contains bioactive compounds which, independently of known photoactivatable mechanisms, potently inhibit cancer cell proliferation and survival through multiple targets.
PMCID: PMC3124362  PMID: 21273604
Medicinal herb; bioactivity; p53 pathway; apoptosis
6.  Transcriptional regulation of the Papilio polyxenes CYP6B1 gene. 
Nucleic Acids Research  1994;22(15):3210-3217.
Detoxification of host plant defensive compounds by larval Lepidoptera is mediated by cytochrome P450 monooxygenases (P450s) such as CYP6B1, which is expressed in Papilio polyxenes (black swallowtail) larvae in response to xanthotoxin, a linear furanocoumarin. Baculovirus-mediated expression of two cloned CYP6B1 cDNAs in lepidopteran cell lines has demonstrated that CYP6B1 isozymes primarily metabolize the linear furanocoumarins, xanthotoxin and bergapten, and not angular furanocoumarins. To characterize the regulatory features of the CYP6B1 transcription unit, we have isolated the first full-length CYP6B1v3 genomic DNA clone from P. polyxenes. The open reading frame of this gene is interrupted by a single intron and is virtually identical to the previously characterized CYP6B1 cDNAs. Primer extension and ribonuclease protection analyses have localized the transcription initiation site to a point 28 nucleotides upstream from the AUG initiation codon. RNase protection analyses on RNA from larvae induced by linear and angular furanocoumarins indicate that transcription of the CYP6B1 gene is induced in insects significantly in response to xanthotoxin and only slightly in response to bergapten. Angular furanocoumarins, such as angelicin, which are not appreciably metabolized by the CYP6B1 gene product, do not significantly induce transcription of this gene. We conclude that this P450 gene is transcriptionally regulated in vivo by at least one of the substrates which the encoded protein metabolizes. Transient expression of CAT fusion constructs in transfected Sf9 lepidopteran cells demonstrates that nucleotides -1 to -838 upstream from the CYP6B1v3 transcription initiation site retain basal and xanthotoxin-inducible transcriptional activities in this heterologous cell line. These data clearly indicate that P. polyxenes has adapted to the presence of furanocoumarins in its host plants by evolving P450 isozymes and regulatory cascades which respond to specific toxins.
Images
PMCID: PMC310298  PMID: 8065937
7.  Ruta graveolens L. toxicity in Vampirolepis nana infected mice 
Indian Journal of Pharmacology  2010;42(6):345-350.
Objective:
To determine possible toxic effects of Ruta graveolens hydroalcoholic extract in gastrointestinal parasitic infection.
Materials and Methods:
A total of 100 g plant leaves and seeds were powdered and extracted with 1500 mL alcohol/water and administered by gavage to Swiss albino mice infected with Vampirolepis nana. Anti-parasitic evaluation and toxicity assays were carried out in six groups of ten animals each. Treatments were scheduled with both the leaves and the seeds’ extracts at doses of 2.5, 5, and 10 mg per gram body weight. Toxicity was comparatively analyzed to a vehicle control group (n = 10) and to a Praziquantel® treated. On the fifth day, all the individuals were killed by euthanasia and parasite scores were correlated, giving rise to a relative percentage of elimination to each treatment. Toxicity was achieved by hematology and by clinical chemistry determinations.
Results:
The use of the R. graveolens hydroalcoholic extract to treat V. nana infected mice resulted in a mild-to-moderate hepatoxicity associated to a poor anti-parasitic effect. The major proglottids elimination (E%) was achieved at the lowest crude extract concentration with a mild anti-parasitic efficacy from the highest dose; that did not cause a significant elimination of parasites. A decrease of circulating polymorphonuclear-neutrophils associated with a normochromic-normocytic anemia was detected as the extract dose was augmented. The blood aspartate-aminotransferase and alanine-aminotransferase tended be slightly augmented with 100 mg R. graveolens extract.
Conclusion:
R. graveolens is an unsafe natural anti-parasitic medicine as its active constituents may be poorly extracted by the popular crude herb infusion. Although it presented a mild anti-parasitic effect in mice, symptoms of natural-products-induced-liver-disease confirmed that its self-medication should be avoided.
doi:10.4103/0253-7613.71898
PMCID: PMC2991689  PMID: 21189902
Anthelmintic activity; natural-products-induced-liver-disease; Ruta graveolens; Vampirolepis nana
8.  In silico Target Fishing for Rationalized Ligand Discovery Exemplified on Constituents of Ruta graveolens 
Planta medica  2008;75(3):195-204.
The identification of targets whose interaction is likely to result in the successful treatment of a disease is of growing interest for natural product scientists. In the current study we performed an exemplary application of a virtual parallel screening approach to identify potential targets for 16 secondary metabolites isolated and identified from the aerial parts of the medicinal plant Ruta graveolens L. Low energy conformers of the isolated constituents were simultaneously screened against a set of 2208 pharmacophore models generated in-house for the in silico prediction of putative biological targets, i. e., target fishing. Based on the predicted ligand-target interactions, we focused on three biological targets, namely acetylcholinesterase (AChE), the human rhinovirus (HRV) coat protein and the cannabinoid receptor type-2 (CB2). For a critical evaluation of the applied parallel screening approach, virtual hits and non-hits were assayed on the respective targets. For AChE the highest scoring virtual hit, arborinine, showed the best inhibitory in vitro activity on AChE (IC50 34.7 μM). Determination of the anti-HRV-2 effect revealed 6,7,8-trimethoxycoumarin and arborinine to be the most active antiviral constituents with IC50 values of 11.98 μM and 3.19 μM, respectively. Of these, arborinine was predicted virtually. Of all the molecules subjected to parallel screening, one virtual CB2 ligand was obtained, i.e., rutamarin. Interestingly, in experimental studies only this compound showed a selective activity to the CB2 receptor (Ki of 7.4 μM) by using a radioligand displacement assay. The applied parallel screening paradigm with constituents of R. graveolens on three different proteins has shown promise as an in silico tool for rational target fishing and pharmacological profiling of extracts and single chemical entities in natural product research.
doi:10.1055/s-0028-1088397
PMCID: PMC3525952  PMID: 19096995
Ruta graveolens L; Rutaceae; pharmacophore modelling; virtual parallel screening; acetylcholinesterase; cannabinoid receptor 2; human rhinovirus coat protein
9.  Nicotiana benthamiana as a Production Platform for Artemisinin Precursors 
PLoS ONE  2010;5(12):e14222.
Background
Production of pharmaceuticals in plants provides an alternative for chemical synthesis, fermentation or natural sources. Nicotiana benthamiana is deployed at commercial scale for production of therapeutic proteins. Here the potential of this plant is explored for rapid production of precursors of artemisinin, a sesquiterpenoid compound that is used for malaria treatment.
Methodology/Principal Findings
Biosynthetic genes leading to artemisinic acid, a precursor of artemisinin, were combined and expressed in N. benthamiana by agro-infiltration. The first committed precursor of artemisinin, amorpha-4,11-diene, was produced upon infiltration of a construct containing amorpha-4,11-diene synthase, accompanied by 3-hydroxy-3-methylglutaryl-CoA reductase and farnesyl diphosphate synthase. Amorpha-4,11-diene was detected both in extracts and in the headspace of the N. benthamiana leaves. When the amorphadiene oxidase CYP71AV1 was co-infiltrated with the amorphadiene-synthesizing construct, the amorpha-4,11-diene levels strongly decreased, suggesting it was oxidized. Surprisingly, no anticipated oxidation products, such as artemisinic acid, were detected upon GC-MS analysis. However, analysis of leaf extracts with a non-targeted metabolomics approach, using LC-QTOF-MS, revealed the presence of another compound, which was identified as artemisinic acid-12-β-diglucoside. This compound accumulated to 39.5 mg.kg−1 fwt. Apparently the product of the heterologous pathway that was introduced, artemisinic acid, is further metabolized efficiently by glycosyl transferases that are endogenous to N. benthamiana.
Conclusion/Significance
This work shows that agroinfiltration of N. bentamiana can be used as a model to study the production of sesquiterpenoid pharmaceutical compounds. The interaction between the ectopically introduced pathway and the endogenous metabolism of the plant is discussed.
doi:10.1371/journal.pone.0014222
PMCID: PMC2997059  PMID: 21151979
10.  Investigation of Two Distinct Flavone Synthases for Plant-Specific Flavone Biosynthesis in Saccharomyces cerevisiae 
Applied and Environmental Microbiology  2005;71(12):8241-8248.
Flavones are plant secondary metabolites that have wide pharmaceutical and nutraceutical applications. We previously constructed a recombinant flavanone pathway by expressing in Saccharomyces cerevisiae a four-step recombinant pathway that consists of cinnamate-4 hydroxylase, 4-coumaroyl:coenzyme A ligase, chalcone synthase, and chalcone isomerase. In the present work, the biosynthesis of flavones by two distinct flavone synthases was evaluated by introducing a soluble flavone synthase I (FSI) and a membrane-bound flavone synthase II (FSII) into the flavanone-producing recombinant yeast strain. The resulting recombinant strains were able to convert various phenylpropanoid acid precursors into the flavone molecules chrysin, apigenin, and luteolin, and the intermediate flavanones pinocembrin, naringenin, and eriodictyol accumulated in the medium. Improvement of flavone biosynthesis was achieved by overexpressing the yeast P450 reductase CPR1 in the FSII-expressing recombinant strain and by using acetate rather than glucose or raffinose as the carbon source. Overall, the FSI-expressing recombinant strain produced 50% more apigenin and six times less naringenin than the FSII-expressing recombinant strain when p-coumaric acid was used as a precursor phenylpropanoid acid. Further experiments indicated that unlike luteolin, the 5,7,4′-trihydroxyflavone apigenin inhibits flavanone biosynthesis in vivo in a nonlinear, dose-dependent manner.
doi:10.1128/AEM.71.12.8241-8248.2005
PMCID: PMC1317445  PMID: 16332809
11.  Up and down: stamen movements in Ruta graveolens (Rutaceae) enhance both outcrossing and delayed selfing 
Annals of Botany  2012;110(5):1017-1025.
Background and Aims
Stamen movements directly determine pollen fates and mating patterns by altering positions of female and male organs. However, the implications of such movements in terms of pollination are not well understood. Recently, complex patterns of stamen movements have been identified in Loasaceae, Parnassiaceae, Rutaceae and Tropaeolaceae. In this study the stamen movements in Ruta graveolens (Rutaceae) and their impact on pollination are determined.
Methods
Pollination effects of stamen movements were studied in Ruta graveolens, in which one-by-one uplifting and falling back is followed by simultaneous movement of all stamens in some flowers. Using 30 flowers, one stamen was manipulated either to be immobilized or to be allowed to move freely towards the centre of the flower but be prevented from falling back. Pollen loads on stigmas and ovule fertilization in flowers with or without simultaneous stamen movement were determined.
Results
Pollen removal decreased dramatically (P < 0·001) when the stamen was stopped from uplifting because its anther was seldom contacted by pollinators. When a stamen stayed at the flower's centre, pollen removal of the next freely moved anther decreased significantly (P < 0·005) because of fewer touches by pollinators and quick leaving of pollinators that were discouraged by the empty anther. Simultaneous stamen movement occurred only in flowers with low pollen load on the stigma and the remaining pollen in anthers dropped onto stigma surfaces after stamens moved to the flower's centre.
Conclusions
In R. graveolens pollen removal is promoted through one-by-one movement of the stamen, which presents pollen in doses to pollinators by successive uplifting of the stamen and avoids interference of two consecutively dehisced anthers by falling back of the former stamen before the next one moves into the flower's centre. Simultaneous stamen movement at the end of anthesis probably reflects an adaptation for late-acting self-pollination.
doi:10.1093/aob/mcs181
PMCID: PMC3448434  PMID: 22875813
Dichogamy; experimental manipulation; pollen presentation; pollen removal; pollination; reproductive assurance; Ruta graveolens; stamen movement
12.  A Review of Coumarin Derivatives in Pharmacotherapy of Breast Cancer 
Current medicinal chemistry  2008;15(26):2664-2679.
The coumarin (benzopyran-2-one, or chromen-2-one) ring system, present in natural products (such as the anticoagulant warfarin) that display interesting pharmacological properties, has intrigued chemists and medicinal chemists for decades to explore the natural coumarins or synthetic analogs for their applicability as drugs. Many molecules based on the coumarin ring system have been synthesized utilizing innovative synthetic techniques. The diversity oriented synthetic routes have led to interesting derivatives including the furanocoumarins, pyranocoumarins, and coumarin sulfamates (COUMATES), which have been found to be useful in photochemotherapy, antitumor and anti-HIV therapy, and as stimulants for central nervous system, antibacterials, anti-inflammatory, anti-coagulants, and dyes. Of particular interest in breast cancer chemotherapy, some coumarins and their active metabolite 7-hydroxycoumarin analogs have shown sulfatase and aromatase inhibitory activities. Coumarin based selective estrogen receptor modulators (SERMs) and coumarin-estrogen conjugates have also been described as potential antibreast cancer agents. Since breast cancer is the second leading cause of death in American women behind lung cancer, there is a strong impetus to identify potential new drug treatments for breast cancer. Therefore, the objective of this review is to focus on important coumarin analogs with antibreast cancer activities, highlight their mechanisms of action and structure-activity relationships on selected receptors in breast tissues, and the different methods that have been applied in the construction of these pharmacologically important coumarin analogs.
PMCID: PMC3772644  PMID: 18991629
Coumarin; breast cancer; sulfatase inhibitor; aromatase inhibitor
13.  Selected phenolic compounds in cultivated plants: ecologic functions, health implications, and modulation by pesticides. 
Environmental Health Perspectives  1999;107(Suppl 1):109-114.
Phenolic compounds are widely distributed in the plant kingdom. Plant tissues may contain up to several grams per kilogram. External stimuli such as microbial infections, ultraviolet radiation, and chemical stressors induce their synthesis. The phenolic compounds resveratrol, flavonoids, and furanocoumarins have many ecologic functions and affect human health. Ecologic functions include defense against microbial pathogens and herbivorous animals. Phenolic compounds may have both beneficial and toxic effects on human health. Effects on low-density lipoproteins and aggregation of platelets are beneficial because they reduce the risk of coronary heart disease. Mutagenic, cancerogenic, and phototoxic effects are risk factors of human health. The synthesis of phenolic compounds in plants can be modulated by the application of herbicides and, to a lesser extent, insecticides and fungicides. The effects on ecosystem functioning and human health are complex and cannot be predicted with great certainty. The consequences of the combined natural and pesticide-induced modulating effects for ecologic functions and human health should be further evaluated.
PMCID: PMC1566369  PMID: 10229712
14.  Enzymatic Properties and Mutational Studies of Chalcone Synthase from Physcomitrella patens 
PpCHS is a member of the type III polyketide synthase family and catalyses the synthesis of the flavonoid precursor naringenin chalcone from p-coumaroyl-CoA. Recent research reports the production of pyrone derivatives using either hexanoyl-CoA or butyryl-CoA as starter molecule. The Cys-His-Asn catalytic triad found in other plant chalcone synthase predicted polypeptides is conserved in PpCHS. Site directed mutagenesis involving these amino acids residing in the active-site cavity revealed that the cavity volume of the active-site plays a significant role in the selection of starter molecules as well as product formation. Substitutions of Cys 170 with Arg and Ser amino acids decreased the ability of the PpCHS to utilize hexanoyl-CoA as a starter molecule, which directly effected the production of pyrone derivatives (products). These substitutions are believed to have a restricted number of elongations of the growing polypeptide chain due to the smaller cavity volume of the mutant’s active site.
doi:10.3390/ijms13089673
PMCID: PMC3431822  PMID: 22949824
chalcone synthase; site-directed mutagenesis; active site; by-products
15.  Biosynthesis of caffeic acid in Escherichia coli using its endogenous hydroxylase complex 
Background
Caffeic acid (3,4-dihydroxycinnamic acid) is a natural phenolic compound derived from the plant phenylpropanoid pathway. Caffeic acid and its phenethyl ester (CAPE) have attracted increasing attention for their various pharmaceutical properties and health-promoting effects. Nowadays, large-scale production of drugs or drug precursors via microbial approaches provides a promising alternative to chemical synthesis and extraction from plant sources.
Results
We first identified that an Escherichia coli native hydroxylase complex previously characterized as the 4-hydroxyphenylacetate 3-hydroxylase (4HPA3H) was able to convert p-coumaric acid to caffeic acid efficiently. This critical enzymatic step catalyzed in plants by a membrane-associated cytochrome P450 enzyme, p-coumarate 3-hydroxylase (C3H), is difficult to be functionally expressed in prokaryotic systems. Moreover, the performances of two tyrosine ammonia lyases (TALs) from Rhodobacter species were compared after overexpression in E. coli. The results indicated that the TAL from R. capsulatus (Rc) possesses higher activity towards both tyrosine and L-dopa. Based on these findings, we further designed a dual pathway leading from tyrosine to caffeic acid consisting of the enzymes 4HPA3H and RcTAL. This heterologous pathway extended E. coli native tyrosine biosynthesis machinery and was able to produce caffeic acid (12.1 mg/L) in minimal salt medium. Further improvement in production was accomplished by boosting tyrosine biosynthesis in E. coli, which involved the alleviation of tyrosine-induced feedback inhibition and carbon flux redirection. Finally, the titer of caffeic acid reached 50.2 mg/L in shake flasks after 48-hour cultivation.
Conclusion
We have successfully established a novel pathway and constructed an E. coli strain for the production of caffeic acid. This work forms a basis for further improvement in production, as well as opens the possibility of microbial synthesis of more complex plant secondary metabolites derived from caffeic acid. In addition, we have identified that TAL is the rate-limiting enzyme in this pathway. Thus, exploration for more active TALs via bio-prospecting and protein engineering approaches is necessary for further improvement of caffeic acid production.
doi:10.1186/1475-2859-11-42
PMCID: PMC3379962  PMID: 22475509
16.  Brassinosteroids Regulate Plant Growth through Distinct Signaling Pathways in Selaginella and Arabidopsis 
PLoS ONE  2013;8(12):e81938.
Brassinosteroids (BRs) are growth-promoting steroid hormones that regulate diverse physiological processes in plants. Most BR biosynthetic enzymes belong to the cytochrome P450 (CYP) family. The gene encoding the ultimate step of BR biosynthesis in Arabidopsis likely evolved by gene duplication followed by functional specialization in a dicotyledonous plant-specific manner. To gain insight into the evolution of BRs, we performed a genomic reconstitution of Arabidopsis BR biosynthetic genes in an ancestral vascular plant, the lycophyte Selaginella moellendorffii. Selaginella contains four members of the CYP90 family that cluster together in the CYP85 clan. Similar to known BR biosynthetic genes, the Selaginella CYP90s exhibit eight or ten exons and Selaginella produces a putative BR biosynthetic intermediate. Therefore, we hypothesized that Selaginella CYP90 genes encode BR biosynthetic enzymes. In contrast to typical CYPs in Arabidopsis, Selaginella CYP90E2 and CYP90F1 do not possess amino-terminal signal peptides, suggesting that they do not localize to the endoplasmic reticulum. In addition, one of the three putative CYP reductases (CPRs) that is required for CYP enzyme function co-localized with CYP90E2 and CYP90F1. Treatments with a BR biosynthetic inhibitor, propiconazole, and epi-brassinolide resulted in greatly retarded and increased growth, respectively. This suggests that BRs promote growth in Selaginella, as they do in Arabidopsis. However, BR signaling occurs through different pathways than in Arabidopsis. A sequence homologous to the Arabidopsis BR receptor BRI1 was absent in Selaginella, but downstream components, including BIN2, BSU1, and BZR1, were present. Thus, the mechanism that initiates BR signaling in Selaginella seems to differ from that in Arabidopsis. Our findings suggest that the basic physiological roles of BRs as growth-promoting hormones are conserved in both lycophytes and Arabidopsis; however, different BR molecules and BRI1-based membrane receptor complexes evolved in these plants.
doi:10.1371/journal.pone.0081938
PMCID: PMC3862569  PMID: 24349155
17.  Escherichia coli as a platform for functional expression of plant P450 carotene hydroxylases 
Carotenoids and their derivatives are essential for growth, development, and signaling in plants and have an added benefit as nutraceuticals in food crops. Despite the importance of the biosynthetic pathway, there remain open questions regarding some of the later enzymes in the pathway. The CYP97 family of P450 enzymes was predicted to function in carotene ring hydroxylation, to convert provitamin A carotenes to nonprovitamin A xanthophylls. However, substrate specificity was difficult to investigate directly in plants, which mask enzyme activities by a complex and dynamic metabolic network. To characterize the enzymes more directly, we amplified cDNAs from a model crop, Oryza sativa, and used functional complementation in Escherichia coli to test activity and specificity of members of Clans A and C. This heterologous system will be valuable for further study of enzyme interactions and substrate utilization needed to understand better the role of CYP97 hydroxylases in plant carotenoid biosynthesis.
doi:10.1016/j.abb.2006.11.019
PMCID: PMC1810121  PMID: 17196929
carotene; P450; CYP97; hydroxylases; vitamin A; Oryza sativa; metabolic engineering; xanthophylls; plants; Escherichia coli functional complementation
18.  Antibacterial activity of methanol extract of Ruta chalapensis (L), Quercus infectoria (Oliver) and Canthium parviflorum (Lam) 
Ancient Science of Life  2009;29(2):28-31.
The present study aimed at evaluating the antibacterial activity of methanol extract of Ruta chalapensis, L., (Rutaceae), Quercus infectoria Oliver., (Fagaceae) and Canthium parviflorum Lam., (Rubiaceae) against Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, Klebsiella oxytocoa, Klebsiella pneumoniae and Proteus mirabilis. The experiment was carried out using disc diffusion method. The results revealed that the methanol extract of aerial parts of Ruta chalepensis (L) presented the highest zone of inhibition against tested pathogens. Other plants showed significant zone of inhibition.
PMCID: PMC3336310  PMID: 22557348
Ruta chalapensis; (L) Quercus infectoria (Oliver); Canthium parviflorum; (Lam) antibacterial activity and zone of inhibition
19.  Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands 
Ecology and Evolution  2013;3(6):1569-1579.
Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability.
doi:10.1002/ece3.571
PMCID: PMC3686192  PMID: 23789068
Clonal reproduction; genetic diversity; insular; microsatellite; rare; Ruta microcarpa
20.  Cholic acid mediates negative feedback regulation of bile acid synthesis in mice 
The Journal of Clinical Investigation  2002;110(8):1191-1200.
Cholesterol is converted into dozens of primary and secondary bile acids through pathways subject to negative feedback regulation mediated by the nuclear receptor farnesoid X receptor (FXR) and other effectors. Disruption of the sterol 12α-hydroxylase gene (Cyp8b1) in mice prevents the synthesis of cholate, a primary bile acid, and its metabolites. Feedback regulation of the rate-limiting biosynthetic enzyme cholesterol 7α-hydroxylase (CYP7A1) is lost in Cyp8b1–/– mice, causing expansion of the bile acid pool and alterations in cholesterol metabolism. Expression of other FXR target genes is unaltered in these mice. Cholate restores CYP7A1 regulation in vivo and in vitro. The results implicate cholate as an important negative regulator of bile acid synthesis and provide preliminary evidence for ligand-specific gene activation by a nuclear receptor.
doi:10.1172/JCI16309
PMCID: PMC150802  PMID: 12393855
21.  A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land 
Biology Direct  2009;4:7.
Background
The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.
Results
We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments.
Conclusion
Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.
Reviewers
This article was reviewed by Purificación López-García, Janet Siefert, and Eugene Koonin.
doi:10.1186/1745-6150-4-7
PMCID: PMC2657906  PMID: 19220881
22.  Anethum graveolens: An Indian traditional medicinal herb and spice 
Pharmacognosy Reviews  2010;4(8):179-184.
Anethum graveolens L. (dill) has been used in ayurvedic medicines since ancient times and it is a popular herb widely used as a spice and also yields essential oil. It is an aromatic and annual herb of apiaceae family. The Ayurvedic uses of dill seeds are carminative, stomachic and diuretic. There are various volatile components of dill seeds and herb; carvone being the predominant odorant of dill seed and α-phellandrene, limonene, dill ether, myristicin are the most important odorants of dill herb. Other compounds isolated from seeds are coumarins, flavonoids, phenolic acids and steroids. The main purpose of this review is to understand the significance of Anethum graveolens in ayurvedic medicines and non-medicinal purposes and emphasis can also be given to the enhancement of secondary metabolites of this medicinal plant.
doi:10.4103/0973-7847.70915
PMCID: PMC3249919  PMID: 22228959
Anethum graveolens; ayurvedic uses; carvone; limonene; monoterpenes; review
23.  Isolation and functional characterization of a cDNA coding a hydroxycinnamoyltransferase involved in phenylpropanoid biosynthesis in Cynara cardunculus L 
BMC Plant Biology  2007;7:14.
Background
Cynara cardunculus L. is an edible plant of pharmaceutical interest, in particular with respect to the polyphenolic content of its leaves. It includes three taxa: globe artichoke, cultivated cardoon, and wild cardoon. The dominating phenolics are the di-caffeoylquinic acids (such as cynarin), which are largely restricted to Cynara species, along with their precursor, chlorogenic acid (CGA). The scope of this study is to better understand CGA synthesis in this plant.
Results
A gene sequence encoding a hydroxycinnamoyltransferase (HCT) involved in the synthesis of CGA, was identified. Isolation of the gene sequence was achieved by using a PCR strategy with degenerated primers targeted to conserved regions of orthologous HCT sequences available. We have isolated a 717 bp cDNA which shares 84% aminoacid identity and 92% similarity with a tobacco gene responsible for the biosynthesis of CGA from p-coumaroyl-CoA and quinic acid. In silico studies revealed the globe artichoke HCT sequence clustering with one of the main acyltransferase groups (i.e. anthranilate N-hydroxycinnamoyl/benzoyltransferase). Heterologous expression of the full length HCT (GenBank accession DQ104740) cDNA in E. coli demonstrated that the recombinant enzyme efficiently synthesizes both chlorogenic acid and p-coumaroyl quinate from quinic acid and caffeoyl-CoA or p-coumaroyl-CoA, respectively, confirming its identity as a hydroxycinnamoyl-CoA: quinate HCT. Variable levels of HCT expression were shown among wild and cultivated forms of C. cardunculus subspecies. The level of expression was correlated with CGA content.
Conclusion
The data support the predicted involvement of the Cynara cardunculus HCT in the biosynthesis of CGA before and/or after the hydroxylation step of hydroxycinnamoyl esters.
doi:10.1186/1471-2229-7-14
PMCID: PMC1847684  PMID: 17374149
24.  Suppression of sterol 12α-hydroxylase transcription by the short heterodimer partner: insights into the repression mechanism 
Nucleic Acids Research  2001;29(19):4035-4042.
Cholesterol conversion to bile acids is subject to a feedback regulatory mechanism by which bile acids down-regulate their own synthesis. This regulation occurs at the level of transcription of several genes encoding enzymes in the bile acid biosynthetic pathway. One of these enzymes is sterol 12α-hydroxylase/CYP8B1 (12α-hydroxylase), the specific enzyme required for cholic acid synthesis. The levels of this enzyme determine the ratio of cholic acid to chenodeoxycholic acid and thus the hydrophobicity of the circulating bile acid pool. Previous studies from this laboratory showed that fetoprotein transcription factor (FTF) is required for 12α-hydroxylase promoter activity and bile acid-mediated regulation. Here, we report that the short heterodimer partner (SHP) suppresses 12α-hydroxylase promoter activity via an interaction with FTF. Hepatic nuclear factor-4 (HNF-4) binds and activates the 12α-hydroxylase promoter and is required for 12α-hydroxylase promoter activity. Although HNF-4 interacts with SHP, it is not involved in SHP-mediated suppression of 12α-hydroxylase promoter activity. FTF and not HNF-4 is the factor involved in regulation of 12α-hydroxylase promoter activity by bile acids through its interaction with SHP. Finally, interaction of SHP with FTF displaces FTF binding to its sites within the 12α-hydroxylase promoter. These results provide insights into the mechanism of action of bile acid-mediated regulation of sterol 12α-hydroxylase transcription.
PMCID: PMC60248  PMID: 11574686
25.  Rapid expression of transgenes driven by seed-specific constructs in leaf tissue: DHA production 
Plant Methods  2010;6:8.
Background
Metabolic engineering of seed biosynthetic pathways to diversify and improve crop product quality is a highly active research area. The validation of genes driven by seed-specific promoters is time-consuming since the transformed plants must be grown to maturity before the gene function can be analysed.
Results
In this study we demonstrate that genes driven by seed-specific promoters contained within complex constructs can be transiently-expressed in the Nicotiana benthamiana leaf-assay system by co-infiltrating the Arabidopsis thaliana LEAFY COTYLEDON2 (LEC2) gene. A real-world case study is described in which we first assembled an efficient transgenic DHA synthesis pathway using a traditional N. benthamiana Cauliflower Mosaic Virus (CaMV) 35S-driven leaf assay before using the LEC2-extended assay to rapidly validate a complex seed-specific construct containing the same genes before stable transformation in Arabidopsis.
Conclusions
The LEC2-extended N. benthamiana assay allows the transient activation of seed-specific promoters in leaf tissue. In this study we have used the assay as a rapid preliminary screen of a complex seed-specific transgenic construct prior to stable transformation, a feature that will become increasingly useful as genetic engineering moves from the manipulation of single genes to the engineering of complex pathways. We propose that the assay will prove useful for other applications wherein rapid expression of transgenes driven by seed-specific constructs in leaf tissue are sought.
doi:10.1186/1746-4811-6-8
PMCID: PMC2845569  PMID: 20222981

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