GarlicESTdb: an online database and mining tool for garlic EST sequences

Background  

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.     

Bioactive polar natural compounds from garlic and onions

Bioactive natural compounds from garlic and onions have been the focus of researches for decades, firstly due to their pharmacological effects, and secondly due to their defence properties against plant diseases. In fact, garlic and onion, belonging to Allium genus, are among the oldest food plants known since ancient times and used as ingredient of many recipes and for therapeutic properties. These plants are well known to produce bioactive apolar sulphur compounds but less is known about their polar natural compounds, such as phenols, sapogenins and saponins, that are more stable to cooking, So, we continued our work on the discovery of polar bioactive metabolites from Allium with the isolation of a number of sapogenins and saponins from the wild onion species Allium elburzense, Allium hirtifolium, Allium atroviolaceum, and Allium minutiflorum, and, more recently, from the cultivated white onion, Allium cepa, and garlic, Allium sativum. In particular, the sapogenins and saponins isolated from A. elburzense and A. hirtifolium, named elburzensosides and hirtifoliosides respectively, exhibited significant antispasmodic properties. In addition, the saponins named minutosides isolated from A. minutiflorum showed promising antimicrobial activity. More recently the phytochemical analysis of A. cepa and A. sativum has been undertaken and afforded the characterization of saponins, phenols and N-cynnamic amides which showed significant antifungal activity.     

What makes Allium species effective against pathogenic microbes?

The antimicrobial activity of garlic (Allium sativum L.) has been known since ancient times. The first citation dates back to the Egyptian period of fifteenth century BC when garlic was reported to be used in folk medicine as a remedy for microbial infections. Scientific investigations on garlic started in 1858 with the work of Pasteur who first noted antibacterial properties of garlic extracts. From that date to the discovery of antibiotics, garlic has been used against amoebic dysentery and epidemic diseases such as typhus, cholera, diphtheria, and tuberculosis. But what makes garlic and Allium species effective against pathogenic microbes? The volatile allicin and other thiosulfinates, giving pungency to Allium plants, are well-studied antimicrobial agents. The thiosulfinates can decompose to form additional sulfur constituents, including diallyl, methyl allyl, and dipropyl mono-, di-, tri- e tetra-sulfides, and (E)- and (Z)-ajoene without losing antimicrobial activity. Besides these compounds, onion and garlic are characterized by polar compounds of steroidal and phenolic origin, often glycosilated, not pungent and more stable during cooking, showing also antimicrobial activity. Recently, there has been increasing scientific attention given to such compounds. Nitrogen organic compounds, like alkaloids and polypeptides, have also been isolated from these plants and have shown antimicrobial activity. In this paper, the literature about the major volatile and non-volatile organic compounds of garlic and other Allium plants has been reviewed. Particular attention is given to the compounds possessing antimicrobial activity and to the correlation between the observed activity and the chemical structure of the tested compounds.     

Development of a biosensor specific for cysteine sulfoxides

S-Alk(en)yl cysteine sulfoxides have been observed in several plants, mainly belonging to the onion family (Alliaceae), which are of high commercial interest (e.g. garlic, Allium sativum). The quality of most garlic containing herbal remedies produced from garlic powder is determined by their content of the cysteine sulfoxide alliin. Therefore, a comprehensive method for the documentation of alliin amounts present in the fresh plant material through to the final remedy is desirable. The newly developed biosensoric method described in this paper was designed in order to fulfil these demands. In contrast to conventional HPLC-methods, neither a pre-column derivatization nor a chromatographic separation are required allowing a high throughput of samples. This technique is based on immobilized alliinase (EC 4.4.1.4), which was combined with an ammonia-gas electrode. The enzyme was either placed in a small cartridge or was immobilized in direct contact of the electrode surface giving detection limits of 3.7 x 10(-7) and 5.9 x 10(-6) M. Founded on these experiments, a pH-sensitive electrolyte/insulator/semiconductor (EIS) layer structure made of Al/p-Si/SiO(2)/Si(3)N(4) was also combined with immobilized alliinase. Measurements could be performed in a range between 1 x 10(-5) and 1 x 10(-3) M alliin. All sensors were operated in the flow-through modus. A high specificity for alliin could be demonstrated for the electrode and a number of garlic samples were analyzed. Results gained with the new method showed a good correlation with those obtained with conventional HPLC-methods. In addition, onion and a variety of wild Allium species were analyzed in order to determine the amount of isoalliin or total cysteine sulfoxides present, respectively.     

The C-S lyases of higher plants: preparation and properties of homogeneous alliin lyase from garlic (Allium sativum)

Alliin lyase from garlic (Allium sativum) has been purified to homogeneity. The purification procedure involves the use of affinity chromatography on concanavalin A-Sepharose 4B. Addition of polyvinylpolypyrrolidone to the homogenizing medium greatly improves the specific activity of the extract. The enzyme is a glycoprotein as seen by its ability to bind to concanavalin A-Sepharose 4B and by its positive periodic acid-Schiff base stain. It has a carbohydrate content of 5.5%. Km values for this enzyme were estimated to be 5.7 mM for S-ethyl-L-cysteine sulfoxide and 3.3 mM for S-allyl-L-cysteine sulfoxide. The molecular weight of this garlic enzyme, as determined by gel filtration, was found to be 85,000; the molecule consists of two equal subunits of Mr 42,000. The amino acid content was found to be similar to that reported previously for onion alliin lyase, although there is twice as much tryptophan in the garlic alliin lyase as in the onion enzyme. By both chemical and spectral methods the enzyme was found to have two molecules of pyridoxal 5-phosphate per enzyme molecule, suggesting one per subunit. There are significant differences in the nature of these findings from those previously reported from this laboratory for the onion enzyme. Studies are in progress to compare further the alliin lyases from garlic and onion.     

The C-S lyases of higher plants. Purification and characterization of homogeneous alliin lyase of leek (Allium porrum)

The characteristic odors of freshly macerated tissue of Allium species such as garlic and onion are due to the action of the enzyme alliin lyase (EC 4.4.1.4) on endogenous S-alkyl-I-cysteine sulfoxides which are present as secondary amino acids yielding volatile sulfur-containing products. Purification and characterization of the alliin lyase of leek ( Allium porrum L.) has been carried out for comparison with the analogous enzymes previously characterized from garlic and onion. The purification involved homogenization, followed by ammonium sulfate fractionation, elution from an hydroxylapatite column, concentration of the active fractions and passage through a concanavalin A-Sepharose 4B affinity column. The purified enzyme was found to be a glycoprotein with a pH optimum for activity of 8.0. Sodium dodecylsulfate-urea polyacrylamide gel electrophoresis gels of the homogeneous leek enzyme showed it consisted of 1 subunit with a molecular weight of 48000. By gel filtration, 2 stable forms of the native enzyme with molecular weights of 386000 and 580000 were found.     

Stemphylium leaf blight of onion

A foliar blight disease of onion (Allium cepa L.) and garlic (Allium sativum L.) hitherto unreported from India has been described from Varanasi, U. P. The infection is confined to the leaves and inflorescence stalks. The conidial stage of the pathogen is more injurious to the plants, whereas the perithecial stage occurs on the inflorescence stalks in isolated locations. The conidiophores and conidia typical of the genus Stemphylium Wallroth are formed during the early development of the disease followed by perithecia predominantly developing on the peduncles. The perithecia were also induced to develop in artificial culture and were identical in diagnostic characters to those from the field. The conidia and ascospores from both host and artificial culture were reciprocally pathogenic to onion and garlic. Morphology of the fruiting structures indicated identity of the pathogen in its conidial stage with Stemphylium vesicarium (Wallroth) Simmons and in the perithecial stage with Pleospora allii (Rabenh.) Ces. and de Not., to which they are referred respectively.     

Agrobacterium tumefaciens-mediated transformation of leek (Allium porrum) and garlic (Allium sativum)

Transgenic leek (Allium porrum) and garlic (Allium sativum) plants have been recovered by the selective culturing of immature leek and garlic embryos via Agrobacterium-mediated transformation using a method similar to that described by Eady et al. (Plant Cell Rep 19:376–381, 2000) for onion transformation. This method involved the use of a binary vector containing the m-gfp-ER reporter gene and nptII selectable marker, and followed the protocol developed previously for the transformation of onions with only minor modifications pertaining to the post-transformation selection procedure which was simplified to have just a single selection regime. Transgenic cultures were selected for their ability to express the m-gfp-ER reporter gene and grown in the presence of geneticin (20 mg/l). The presence of transgenes in the genome of the plants was confirmed using TAIL-PCR and Southern analysis. This is the first report of leek and true seed garlic transformation. It now makes possible the integration of useful agronomic and quality traits into these crops.     

Biosynthesis of the flavour precursors of onion and garlic

Onion (Allium cepa), garlic (A. sativum) and other Alliums are important because of the culinary value of their flavours and odours. These are characteristic of each species and are created by chemical transformation of a series of volatile sulphur compounds generated by cleavage of relatively stable, odourless, S-alk(en)yl cysteine sulphoxide flavour precursors by the enzymes alliinase and lachrymatory-factor synthase. These secondary metabolites are S-methyl cysteine sulphoxide (MCSO, methiin; present in most Alliums, some Brassicaceae), S-allyl cysteine sulphoxide (ACSO, alliin; characteristic of garlic), S-trans-prop-1-enyl cysteine sulphoxide (PECSO, isoalliin; characteristic of onion), and S-propyl cysteine sulphoxide (PCSO, propiin; in onion and related species). Information from studies of the transformation of putative biosynthetic intermediates, radiolabelling, and from measurements of sulphur compounds within onion and garlic have provided information to suggest a biosynthetic pathway. This may involve alk(en)ylation of the cysteine in glutathione, followed by cleavage and oxidation to form the alk(en)yl cysteine sulphoxide flavour precursors. There is also evidence that synthesis of the flavour precursors may involve (thio)alk(en)ylation of cysteine or a precursor such as O-acetyl serine. Both routes may occur depending on the physiological state of the tissue. There are indications from the effects of environmental factors, such as the availability of sulphur, that control of the biosynthesis of each flavour precursor may be different. Cysteine and glutathione metabolism are discussed to indicate parallels with Allium flavour precursor biosynthesis. Finally, possible avenues for exploration to determine the origin in planta of the alk(en)yl groups are suggested.     

Efficient Agrobacterium tumefaciens-mediated transformation and regeneration of garlic (Allium sativum) immature leaf tissue

Transgenic garlic (Allium sativum) plants have been recovered directly from immature leaf material by selective culture following Agrobacterium-mediated transformation. This method involved the use of a binary vector containing the mgfp-ER reporter gene and hpt selectable marker, and followed a similar protocol developed previously for the transformation of immature onion embryos. The choice of tissue and post-transformation selection procedure resulted in a large increase in recovery of transgenic plants compared with previously confirmed allium transformation protocols. The presence of transgenes in the genome of the plants was confirmed using Southern analysis. This improvement in frequency and the use of clonal commercial “Printanor” germplasm now makes possible the integration of useful agronomic and quality traits into this crop.     

The Oligosaccharide Units of the Xyloglucans in the Cell Walls of Bulbs of Onion, Garlic and their Hybrid

Xyloglucans were isolated from the 24% KOH-soluble fractionof the cell walls of bulbs of onion (Allium cepa), garlic (Alliumsativum) and their hybrid. The polysaccharides yielded singlepeaks upon gel filtration with average moleular weights of 65,000for onion, 55,000 for garlic and 82,000 for the hybrid. Compositionalanalysis of the oligosaccharide units after digestion with anendo-1,4-ß-glucanase from Streptomyces indicated thatthe polysaccharides were constructed of four kinds of repeatingoligosaccharide unit, namely, a decasaccharide (glucose/xylose/galactose/fucose,4 : 3 : 2 : 1), a nonasaccharide (glucose/xylose/galactose/fucose,4 : 3 : 1 : 1), an octasaccharide (glucose/xylose/galactose,4 : 3 : 1 ) , and a heptasaccharide (glucose/xylose, 4 : 3).The xyloglucan from the hybrid contained highly fucosylatedunits that resembled those from onion rather than from garlic.The analysis also revealed that the xyloglucans from Alliumspecies contain highly substituted xylosyl residues with fucosyl-galactosylresidues, suggesting that these monocotyledonous plants resembledicotyledons in the structural features of their xyloglucans. (Received November 1, 1993; Accepted June 16, 1994)     

Synergism between plant extract and antimicrobial drugs used on Staphylococcus aureus diseases

Searches for substances with antimicrobial activity are frequent, and medicinal plants have been considered interesting by some researchers since they are frequently used in popular medicine as remedies for many infectious diseases. The aim of this study was to verify the synergism between 13 antimicrobial drugs and 8 plant extracts--"guaco" (Mikania glomerata), guava (Psidium guajava), clove (Syzygium aromaticum), garlic (Allium sativum), lemongrass (Cymbopogon citratus), ginger (Zingiber officinale), "carqueja" (Baccharis trimera), and mint (Mentha piperita)--against Staphylococcus aureus strains, and for this purpose, the disk method was the antimicrobial susceptibility test performed. Petri dishes were prepared with or without dilution of plant extracts at sub-inhibitory concentrations in Mueller-Hinton Agar (MHA), and the inhibitory zones were recorded in millimeters. In vitro anti-Staphylococcus aureus activities of the extracts were confirmed, and synergism was verified for all the extracts; clove, guava, and lemongrass presented the highest synergism rate with antimicrobial drugs, while ginger and garlic showed limited synergistic capacity.     

Agrobacterium tumefaciens-mediated transformation and regeneration of herbicide resistant onion (Allium cepa) plants

Transgenic onion plants (Allium cepa) tolerant to herbicides containing active ingredients glyphosate and phosphinothricin were recovered from immature embryos of open pollinated and hybrid parent onion lines at a maximum transformation frequency of 0.9%. Transformants of different onion cultivars, grown on different selective agents and confirmed by Southern analysis, thrived with no apparent ill effects when sprayed with the respective herbicides at double the recommended field dosage for weed eradication. This study demonstrates that the transformation process described previously can be used with different selective agents and is cultivar independent.     

Comparative effects of mono-, di-, tri-, and tetrasulfides derived from plants of the Allium family: redox cycling in vitro and hemolytic activity and Phase 2 enzyme induction in vivo

Epidemiological evidence indicates that a high dietary intake of plants of the Allium family, such as garlic and onions, decreases the risk of cancer in humans. It has been suggested that this effect is due to the ability of the aliphatic mono-, di-, tri-, and tetrasulfides derived from these vegetables to increase tissue activities of Phase 2 detoxification enzymes. In contrast, toxic effects have been recorded in domestic and farm animals after the consumption of garlic or onions, involving oxidative damage to erythrocytes and consequent hemolytic anemia. This effect again has been attributed to the aliphatic sulfides. In the present study, the ability of sulfides derived from garlic and onions to generate "active oxygen" species and cause oxidative damage to erythrocytes in vitro has been compared, together with their ability to cause hemolytic anemia and increase the activity of the Phase 2 enzymes quinone reductase (QR) and glutathione S-transferase (GST) in rats. Monosulfides were without significant effect on any parameter. Di-, tri-, and tetrasulfides generated hydrogen peroxide in the presence of GSH and hemoglobin and caused oxidative damage to erythrocytes in vitro. The activity decreased in the order of tetra- > tri- > disulfide, with the allyl compounds being more potent than the propyl. In vivo, both allyl and propyl tri- and tetrasulfides were powerful hemolytic agents. In contrast, only the allyl sulfides increased the activities of QR and GST; the propyl derivatives were completely without effect. Allyl and propyl tri- and tetrasulfides, thus, may contribute to the toxic effects of Allium vegetables, while only the allyl derivatives are effective in increasing tissue activities of cancer-protective enzymes.     

Antithrombotic and anticancer effects of garlic-derived sulfur compounds: a review

Garlic (Allium sativum L.) has a long history as being a food having a unique taste and odor along with some medicinal qualities. Modern scientific research has revealed that the wide variety of dietary and medicinal functions of garlic can be attributed to the sulfur compounds present in or generated from garlic. Although garlic produces more than 20 kinds of sulfide compounds from a few sulfur-containing amino acids, their functions are different from one another; e.g., allicin, methyl allyl trisulfide, and diallyl trisulfide have antibacterial, antithrombotic, and anticancer activities, respectively. The present paper reviews the physiological functions of garlic in the limited study fields of its antithrombotic and anticancer effects. Before describing these effects, however, we will discuss briefly some characteristics of garlic as a plant and some modes of absorption of orally-administered sulfur compounds from garlic.     

Compounds from Allium species with cytotoxic and antimicrobial activity

Garlic (Allium sativum L.) is a bulb-shaped plant belonging to the Allium genus which also includes onions (Allium cepa L.), leek (Allium ampeloprasum L. var. porrum Gay), shallot (Allium ascalonicum L), scallion (A. fistulosum L.) and chives (Allium schoenoprasum L.). The biological activity of garlic has been known since ancient times. Babylonians, Egyptians, Phoenicians, Greeks and Romans used garlic as a remedy for intestinal disorders, respiratory infections, skin diseases, bacterial infections, worms, wounds and tumors. In particular, before the discovery of antibiotics, garlic has been used against amoebic dysentery and epidemic diseases such as typhus, cholera, diphtheria, and tuberculosis. To date, more than 3,000 publications scientifically supported the use of garlic in the ethno-medicine. But what makes garlic and Allium species effective against cancer? The effect of garlic may arise from its antibacterial properties or from its ability to block formation on cancer-causing substances, half the activation of cancer causing substances, enhance DNA repair, reduce cell proliferation or induce cell death. Epidemiological studies have found that an increase of consumptions of Allium spp. reduce the risk of prostate and gastric cancers and this has been mainly related to two main classes of compounds: the apolar sulphur compounds and the polar saponins. These latter compounds, compared to the more studied thiosulphinates, have the advantages of not being pungent and more stable during cooking. Recently, there has been increasing scientific attention given to such compounds. In this paper, the literature about the major volatile and non-volatile organic compounds of garlic and other Allium plants has been reviewed. Particular attention is given to the compounds possessing antibacterial and cytotoxic activity in garlic and in the other Allium species and their mechanism of action.     

Construction of SSR-based chromosome map in bunching onion (Allium fistulosum)

We have constructed a linkage map of bunching onion (Allium fistulosum L., 2n = 16) using an F(2) population of 225 plants. The map consists of 17 linkage groups with 212 bunching onion SSR markers and 42 bulb onion (A. cepa L.) SSR, InDel, CAPS or dCAPS markers, covering 2,069 cM. This is the first report of a linkage map mainly based on SSR markers in the genus Allium. With the 103 anchor markers [81 bunching onion SSRs, 11 bulb onion SSRs and 11 bulb onion non-SSRs (1 InDel, 9 CAPSs and 1 dCAPS)] whose chromosome assignments were identified in A. cepa and/or A. fistulosum, via the use of several kinds of Allium alien addition lines, 16 of the 17 linkage groups were connected to the 8 basic chromosomes of A. cepa.     

Identification of aster yellows phytoplasma in garlic and green onion by PCR-based methods

In the summer of 1999, typical yellows-type symptoms were observed on garlic and green onion plants in a number of gardens and plots around Edmonton, Alberta, Canada. DNA was extracted from leaf tissues of evidently healthy and infected plants. DNA amplifications were conducted on these samples, using two primer pairs, R16F2n/R2 and R16(1)F1/R1, derived from phytoplasma rDNA sequences. DNA samples of aster yellows (AY), lime witches'-broom (LWB) and potato witches'-broom (PWB) phytoplasmas served as controls and were used to determine group relatedness. In a direct polymerase chain reaction (PCR) assay, DNA amplification with universal primer pair R16F2n/R2 gave the expected amplified products of 1.2 kb. Dilution (1/40) of each of the latter products were used as template and nested with specific primer pair R16(1)F1/R1. An expected PCR product of 1.1 kb was obtained from each phytoplasma-infected garlic and green onion samples, LWB and AY phytoplasmas but not from PWB phytoplasma. An aliquot from each amplification product (1.2 kb) with universal primers was subjected to PCR-based restriction fragment length polymorphism (RFLP) to identify phytoplasma isolates, using four restriction endonucleases (AluI, KpnI, MseI and RsaI). DNA amplification with specific primer pair R16(1)F1/R1 and RFLP analysis indicated the presence of AY phytoplasma in the infected garlic and green onion samples. These results suggest that AY phytoplasma in garlic and green onion samples belong to the subgroup 16Sr1-A.     

A PCR-based marker system monitoring CMS-(S), CMS-(T) and (N)-cytoplasm in the onion ( Allium cepa L.)

The chimerical mitochondrial CMS(1)-specific sequence in chives ( Allium schoenoprasum) was used to develop a PCR-marker that distinguishes both male-sterility inducing cytoplasms, CMS-(S) and CMS-(T), from the normal cytoplasm in onion ( Allium cepa). In combination with a previously described marker for CMS-(S), which anchors in the upstream region of the mitochondrial gene cob, all of the three known cytoplasms in the onion are distinguishable. The PCR-marker system was tested in 361 onion plants, which were selected from F(1)-hybrids and different open-pollinated varieties. The latter are mainly landraces from Turkey, in which all three cytoplasm types were detected.     

Onion and garlic extracts lessen cadmium-induced nephrotoxicity in rats

Cadmium (Cd) is a well-known nephrotoxicant inducing kidney damage via oxidative stress. Since kidney is the critical target organ of Cd toxicity, this study was designed to evaluate the protective effects of onion (Allium cepa L.) and garlic (Allium sativum L.) aqueous extracts on Cd-induced renal oxidative stress in male Wistar rats. The control group received double distilled water alone and Cd group was challenged with 3CdSO₄ · 8H₂O (as Cd) (1.5 mg/100 g bw/day per oral) alone. Extract-treated groups were pre-treated with varied doses (0.5 ml and 1.0 ml/100 g bw/day per oral) of onion and/or garlic extract for 1 week after which they were co-treated with Cd (1.5 mg/100 g bw/day per oral) for 3 weeks. The results showed that the levels of renal lipid peroxidation (LPO) and glutathione-S transferase (GST) were significantly (P < 0.001) increased in rats that received Cd alone relative to the control group. More so, the levels of renal glutathione (GSH), superoxide dismutase (SOD), catalase (CAT) and Na⁺/K⁺-ATPase were significantly (P < 0.001) decreased in rats that received Cd alone. Treatment of Cd-intoxicated rats with varied doses of onion and/or garlic extract significantly (P < 0.05) restored the alterations in these parameters relative to the group that received Cd alone. While treatment with high dose of onion extract exerted a significant dose-dependent restoration of these parameters, treatment with high dose of garlic elicited a pro-oxidant effect, relative to their respective low dose. Our study suggests that onion and garlic extracts may exert their protective effects via reduction in LPO and enhanced antioxidant defense. These extracts may, therefore, be useful nutritional option in alleviating Cd-induced renal damage.