Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos

PREMISE

Plants with stiff, leathery leaves pose a challenge for standard DNA extraction protocols. These tissues are recalcitrant to mechanical disruption via TissueLyser (or analogous devices) and are often high in secondary metabolites. These compounding factors result in low yields, which may be sufficient for PCR amplification but are generally inadequate for genomic applications that require large quantities of high-quality DNA. Cycads in the genus Encephalartos exemplify these challenges, as this group of plants is fortified for life in harsh, dry habitats with notoriously thick and rigid leaves.

METHODS AND RESULTS

Using a DNA extraction kit, we tested three methods of mechanical disruption and examined the differences between stored vs. freshly collected samples and mature vs. senescing leaflets. We found that the manual method of pulverizing tissue yields the highest concentrations of DNA, and that both senescing leaflets and leaflet tissue that has been stored for extended periods yield sufficient DNA for genomic analyses.

CONCLUSIONS

These findings shed light on the feasibility of using senescing leaves and/or tissue that has been stored on silica for long periods of time when attempting to extract large amounts of DNA. We provide here an optimized DNA extraction protocol that can be applied to cycads and other plant groups with tough or rigid leaves.

Chemical Constituents and Their Production in Mexican Oaks (Q. Rugosa, Q. Glabrescens and Q. Obtusata)

Mexico is considered one of the main regions of diversification of the genus Quercus (oaks). Oak species are one of the most important tree groups, particularly in temperate forests, due to its diversity and abundance. Some studies have shown that oak contains specialized metabolites with medicinal importance. In this work, the acetonic extract from leaves of three Mexican oaks (Quercus rugosa, Q. glabrescens, and Q. obtusata) was separated using thin-layer chromatography and column chromatography. Chemical identification of the major compounds was determined using high-performance liquid chromatography and nuclear magnetic resonance. Nineteen compounds were identified, three belonging to the terpenoid family (ursolic acid, β-amyrin, and β-sitosterol) and 16 from the phenolic family. Of the isolated compounds, seven are new reports for oak species (scopoletin, ursolic acid, β-amyrin, luteolin-7-O-glucoside, kaempferol-3-O-sophoroside, kaempferol-3-O-glucoside, and kaempferol-3-O-sambubioside). More compounds were identified in Q. rugosa followed by Q. glabrescens and then Q. obtusata. The characterization of specialized metabolites in oak species is relevant, from both phytocentric and anthropocentric perspectives.

A Comprehensive Review of Phytochemistry and Biological Activities of Quercus Species

The Quercus genus provides a large amount of biomaterial with many applications in fields like pharmaceutics, cosmetics, and foodstuff areas. Due to the worldwide dissemination of the genus, many species were used for centuries in traditional healing methods or in the wine maturing process. This review aims to bring together the results about phytoconstituents from oak extracts and their biological applicability as antioxidants, antimicrobial, anticancer, etc. The literature data used in this paper were collected via PubMed, Scopus, and Science Direct (2010–June 2020). The inclusion criteria were papers published in English, with information about phytoconstituents from Quercus species (leaves, bark and seeds/acorns) and biological activities such as antioxidant, antibacterial, antiobesity, anti-acne vulgaris, antifungal, anticancer, antiviral, antileishmanial, antidiabetic, anti-inflammatory. The exclusion criteria were the research of other parts of the Quercus species (e.g., galls, wood, and twigs); lack of information about phytochemistry and biological activities; non-existent Quercus species reported by the authors. The most studied Quercus species, in terms of identified biomolecules and biological activity, are Q. brantii, Q. infectoria and Q. robur. The Quercus species have been reported to contain several phytoconstituents. The main bioactive phytochemicals are phenolic compounds, volatile organic compounds, sterols, aliphatic alcohols and fatty acids. The, Quercus species are intensely studied due to their antioxidant, anti-inflammatory, antimicrobial, and anticancer activities, provided by their phytochemical composition. The general conclusion is that oak extracts can be exploited for their biological activity and can be used in research fields, such as pharmaceutical, nutraceutical and medical.

Antimicrobial Activities of Ellagitannins against Clostridiales perfringens, Escherichia coli, Lactobacillus plantarum and Staphylococcus aureus

In this study, we tested the growth inhibition effect of 22 individual ellagitannins and of pentagalloylglucose on four bacterial species, i.e., Clostridiales perfringens, Escherichia coli, Lactobacillus plantarum and Staphylococcus aureus. All tested compounds showed antimicrobial effects against S. aureus, and almost all against E. coli and C. perfringens. For L. plantarum, no or very weak growth inhibition was detected. The level of inhibition was the greatest for S. aureus and the weakest for C. perfringens. For S. aureus, the molecular size or flexibility of ellagitannins did not show a clear relationship with their antimicrobial activity, even though rugosins E and D and pentagalloylglucose with four or five free galloyl groups had a stronger growth inhibition effect than the other ellagitannins with glucopyranose cores but with less free galloyl groups. Additionally, our results with S. aureus showed that the oligomeric linkage of ellagitannin might have an effect on its antimicrobial activity. For E. coli, the molecular size, but not the molecular flexibility, of ellagitannins seemed to be an important factor. For C. perfringens, both the molecular size and the flexibility of ellagitannin were important factors. In previous studies, corilagin was used as a model for ellagitannins, but our results showed that other ellagitannins are much more efficacious; therefore, the antimicrobial effects of ellagitannins could be more significant than previously thought.

Partition Coefficients (logP) of Hydrolysable Tannins

The partition coefficients (logP) between n-octanol and water of 47 purified and characterized hydrolysable tannins were measured with the shake flask method utilizing UPLC and HPLC with UV detection. Results show that galloyl glucoses and gallotannins are clearly more hydrophobic than ellagitannins but the differences in hydrophobicity within ellagitannins are more varied than within galloyl glucoses or gallotannins. Most notable structural features that were found to influence the hydrophobicity of ellagitannins were the number of free galloyl groups, acyclic versus cyclic polyol, substitution of the anomeric position of glucose and ⁴C₁ versus ¹C₄ conformation of the glucopyranose core.

Medicinal Uses, Phytochemistry, and Pharmacological Activities of Quercus Species

Quercus species, also known as oak, represent an important genus of the Fagaceae family. It is widely distributed in temperate forests of the northern hemisphere and tropical climatic areas. Many of its members have been used in traditional medicine to treat and prevent various human disorders such as asthma, hemorrhoid, diarrhea, gastric ulcers, and wound healing. The multiple biological activities including anti-inflammatory, antibacterial, hepatoprotective, antidiabetic, anticancer, gastroprotective, antioxidant, and cytotoxic activities have been ascribed to the presence of bioactive compounds such as triterpenoids, phenolic acids, and flavonoids. This paper aimed to provide available information on the medicinal uses, phytochemicals, and pharmacology of species from Quercus. However, further investigation is needed to fully clarify the mode of action of its bioactive compounds and to evaluate in vivo chronic toxicity, before exploring their potential use as a supplement in functional foods and natural pharmaceutics.

Ellagitannins Inhibit the Exsheathment of Haemonchus contortus and Trichostrongylus colubriformis Larvae: The Efficiency Increases Together with the Molecular Size

Worldwide, parasitic gastrointestinal nematodes continue to threaten animal health, welfare, and production in outdoor breeding systems of small ruminants. For more than 50 years, the control of these parasitic worms has relied on the use of commercial synthetic anthelmintics. However, anthelmintic resistance in worm populations is nowadays widespread and requires novel solutions. The use of tannin-rich plants has been suggested as an alternative to synthetic anthelmintics to control gastrointestinal nematodes. The majority of previous studies have focused on the activity of proanthocyanidins (syn condensed tannins), and less is known about ellagitannins. In this study, the effects of 30 structurally unique ellagitannins on the exsheathment of third-stage infective larvae were examined on Haemonchus contortus and Trichostrongylus colubriformis by the in vitro larval exsheathment inhibition assay. Ellagitannins were found to be promising natural anthelmintics as they showed direct inhibition on larval exsheathment for both nematode species. In general, ellagitannins were more efficient at inhibiting the exsheathment of H. contortus larvae than those of T. colubriformis. The efficiency of inhibition increased as the degree of oligomerization or the molecular weight of the ellagitannin increased. Otherwise, we found no other structural features of ellagitannins that significantly affected the anthelmintic activity on the third-stage infective larvae. The effective concentrations were physiologically relevant and should be achievable in the gastrointestinal tract also in in vivo conditions.

Oxidation of the Oak Ellagitannin, Vescalagin

Vescalagin (1) is a major ellagitannin from young spring leaves of Quercus glauca; however, the amount of 1 decreases as the leaves mature with a concomitant rise in the levels of catechin (3) and procyanidins. In this report, the chemical mechanism responsible for the degradation of 1 was investigated. In vitro model experiments indicated that initially a polyphenol oxidase oxidizes the catechin B-ring, and the resulting catechin o-quinone oxidizes one of the pyrogallol rings of 1 to give a cyclopenten-1,2-dione-type product 4. The presence of 4 in young oak leaves was confirmed by the detection of 4 and its quinoxaline derivative 4a. Furthermore, it was demonstrated that the cyclopenten-1,2-dione moiety of 4 nonenzymatically reacted with the catechin A-ring to yield the conjugate 5. Similar conjugations probably occur with procyanidins; thus, these reactions are possibly responsible for the decrease in the levels of 1 in leaves. The same cyclopenten-1,2-dione product 4 was also generated by treatment of 1 with a wood-rotting mushroom, Lentinula edodes, and further oxidative cleavage of a second pyrogallol ring of 4 was also observed. The results indicate the presence of a common degradation mechanism of 1 by plants and microbes.

Ellagitannins with Glucopyranose Cores Have Higher Affinities to Proteins than Acyclic Ellagitannins by Isothermal Titration Calorimetry

The thermodynamics of the interactions of different ellagitannins with two proteins, namely, bovine serum albumin (BSA) and gelatin, were studied by isothermal titration calorimetry. Twelve individual ellagitannins, including different monomers, dimers, and a trimer, were used. The studies showed that several structural features affected the interaction between the ellagitannin and the protein. The interactions of ellagitannins with proteins were stronger with gelatin than with BSA. The ellagitannin-gelatin interactions contained both the primary stronger and the secondary weaker binding sites. The ellagitannin-BSA interactions showed very weak secondary interactions. The ellagitannins with glucopyranose cores had stronger interaction than C-glycosidic ellagitannins with both proteins. In addition, the observed enthalpy change increased as the degree of oligomerization increased. The stronger interactions were also observed with free galloyl groups in the ellagitannin structure and with higher molecular flexibility. Other smaller structural features did not show any overall trend.

Comprehensive analysis of chestnut tannins by reversed phase and hydrophilic interaction chromatography coupled to ion mobility and high resolution mass spectrometry

In this study, we report a methodology based on reversed phase LC (RP-LC) and hydrophilic interaction chromatography (HILIC) separations coupled to ion mobility (IM) and high resolution mass spectrometry (HR-MS) for the detailed analysis of hydrolysable tannins. The application of this approach to the analysis of an industrial chestnut (Castanea sativa, wood chips) tannin extract is demonstrated. A total of 38 molecular species, including a large number or isomers, were identified in this sample based on HR-MS^(E) and UV absorption spectral information as well as retention behaviour in both separation modes. In total, 128 and 90 isomeric species were resolved by RP- and HILIC-LC-IM-TOF-MS, respectively. The combination of low- and high collision energy mass spectral data with complementary chromatographic separations allowed tentative and putative identification of twenty molecular species, comprising 78 isomers, in chestnut for the first time. Ion mobility resolved six new dimeric and trimeric vescalagin conformers with unique arrival (drift) times, including new conformers of roburin A-D which were not separated using either RP-LC or HILIC. HILIC was found to be the preferred separation mode for the analysis of vescalagin derivatives, while RP-LC is preferred for the analysis of ellagitannins with a cyclic glucose core. For the complete separation of the galloyl glucose species, comprehensive HILIC × RP-LC separation would be required.

Ellagitannins from the Onagraceae Decrease the Performance of Generalist and Specialist Herbivores

Phenolics have a role in defenses against herbivores, but the defensive functions of specific groups of phenolics are still poorly understood. For example, ellagitannins (a type of hydrolyzable tannin) are predicted to decrease insect herbivore performance, but the effect of different types of ellagitannins on generalist and specialist herbivores has rarely been assessed. Here, we test the effects of the dominant oligomeric ellagitannins of Oenothera biennis and other Onagraceae on herbivore performance. We fed artificial diets containing between 1 and 100 mg/g of polyphenol fractions comprised of varying amounts and compositions of dimeric oenothein B, the trimeric oenothein A and larger oligomers, to one generalist (Spodoptera exigua) and one specialist (Schinia florida) insect herbivore species. We compared the effects of these ellagitannin fractions on herbivore performance to the effects of artificial diet containing total phenolic extracts from O. biennis, which contained these ellagitannins as well as many additional phenolic metabolites including flavonoid glycosides and caffeic acid derivatives. Both the ellagitannin fractions and O. biennis phenolic extracts had strong negative effects on S. exigua and S. florida performance, with stronger effects on the generalist herbivore. Differences between the effects of the various ellagitannin fractions were small and depended on insect life stage. The defensive effects of these ellagitannins were large, with lethal concentrations as low as 0.1% of the diet. These results highlight the important defensive function of ellagitannins against specialist and generalist herbivores and the need to characterize the effects of these understudied phenolics.

Variability in Foliar Ellagitannins of Hippophaë rhamnoides L. and Identification of a New Ellagitannin, Hippophaenin C

Berries of common sea-buckthorn (Hippophaë rhamnoides L.) are well-known and used for their bioactive components, and while there is a considerable amount of research on the leaves as well, their ellagitannins (ETs) have not been a prominent focus of research. We identified and quantified ten major hydrophilic polyphenols, all ETs, in H. rhamnoides leaves and compared their abundance between 58 plant individuals. Of these compounds, hippophaenin C was characterized as a new ellagitannin by various spectrometric methods. The total concentrations of ETs ranged from 42.5 mg g^-1 dry weight (DW) to 109.1 mg g^-1 DW between individual plants. Among the ETs, hippophaenin C, stachyurin, and casuarinin were on average the most abundant compounds. Sexes did not differ significantly, while cultivars showed variation in some ETs. These results suggest that H. rhamnoides leaves could be a potential and rich source of several ETs.

Topology of syngameons

Syngameons are sets of species linked by interspecific hybridization. Common observations regarding the structure of syngameons are that hybridization propensity is not uniform across species and that patterns of hybridization are dominated by a few species. I use computer simulations to test these claims in naturally occurring syngameons selected from the literature and from personal observation. Natural syngameons, especially those involving plants, typically exhibit nonrandom structure: The first three order statistics for the number of hybrid partners and the variance in the number of hybrid partners are larger than chance alone would predict. The structure of two insect syngameons examined is not significantly different from random. To test a hypothesis that variation in hybridization propensity across species in natural syngameons is simply an artifact of hybridization opportunity, I examine the structure of four artificial syngameons (fertility relationships) produced by full diallel crosses. Three of four artificial syngameons exhibit nonrandom structure, as the observed variation in number of successful crosses is larger than chance alone would predict. In general, there are no significant results involving the order statistics. Finally, I discuss biogeographic, ecological, and phylogenetic hypotheses for variation in hybridization propensity across species in natural syngameons.

The Oxidative Activity of Ellagitannins Dictates Their Tendency To Form Highly Stabilized Complexes with Bovine Serum Albumin at Increased pH

Many food and forage plants contain tannins, high molecular weight polyphenols that characteristically interact strongly with protein, forming complexes that affect taste, nutritional quality, and the health of the consumer. In the present study, the interaction between bovine serum albumin (BSA) and each of seven hydrolyzable tannins or epigallocatechin gallate was examined. The objective was to define the effect of tannin oxidation, measured as oxidative activity (browning) or as oxidizability (degradation monitored by HPLC), on the formation on highly stabilized tannin-protein complexes and to determine how the reaction depended on the pH conditions. Gel electrophoresis and MALDI-TOF-MS were used to assess the formation of tannin-protein complexes. The results showed that tannin oxidizability was directly correlated with the tendency of the tannins to form highly stabilized complexes with BSA at increased pH (7.6). However, at slightly lower pH (6.7), other tannin features, such as the size and flexibility of the tannin, appeared to dictate the formation of highly stabilized tannin-protein complexes.

Rapid estimation of the oxidative activities of individual phenolics in crude plant extracts

Previous studies of purified phenolic compounds have revealed that some phenolics, especially ellagitannins, can autoxidise under alkaline conditions, which predominate in the midgut of lepidopteran larvae. To facilitate screening for the pro-oxidant activities of all types of phenolic compounds from crude plant extracts, we developed a method that combined our recent spectrophotometric bioactivity method with an additional chromatographic step via UPLC-DAD-MS. This method allowed us to estimate the total pro-oxidant capacities of crude extracts from 12 plant species and to identify the individual phenolic compounds that were responsible for the detected activities. It was found that the pro-oxidant capacities of the plant species (i.e., the concentrations of the easily-oxidised phenolics) varied from 0 to 57 mg/g dry wt, representing from 0% to 46% of the total phenolics from different species. UPLC-DAD-MS analysis revealed that most flavonol and flavone glycosides were only slightly affected by alkaline conditions, thus indicating their low pro-oxidant activity. Interestingly, myricetin-type compounds differed from the other flavonoids, as their concentrations decreased strongly due to alkaline incubation. The same effect was detected for hydrolysable tannins and prodelphinidins, suggesting that a pyrogallol sub-structure could be a key structural component that partially explains their easy oxidation at high pH. Other types of phenolic compounds, such as hydroxycinnamic acids, were relatively active, as well. These findings demonstrate that this method displays the potential to identify most of the active and inactive pro-oxidant phenolic compounds in various plant species.

Odor uniformity among tomato individuals in response to herbivore depends on insect species

Plants produce specific volatile organic compound (VOC) blends in response to herbivory. Herbivore-induced blends may prime the plant for future attack or attract carnivorous insects; these responses have been considered adaptive for plants. If herbivores differentially modify the VOC emission among individuals within a group of plants they feed upon, then plant responses to herbivores will not only produce specific blends but also variation in odor among individuals, i.e. individuals smell the same, then having a uniform odor. We investigated the VOC emission variation or uniformity among tomato individuals (Solanum lycopersicum L. cv. Castlemart) in response to moderate wounding by (1) nymphs of the psyllid Bactericera cockerelli (Sulc.) (TP); (2) Lepidoptera chewing-feeding larvae of Fall Armyworm (Spodoptera frugiperda Smith) (FAW) and (3) of Cabbage Looper (Trichoplusia ni Hübner) (CL), and (4) mechanical damage (MD). We used a ratio-based analysis to compare the fold-change in concentration from constitutive to induced VOC emission. We also used size and shape analysis to compare the emission of damaged and non-damaged individuals. Aside of finding herbivore-specific blends in line with other studies, we found patterns not described previously. We detected constitutive and induced odor variation among individuals attacked by the same herbivore, with the induced odor uniformity depending on the herbivore identity. We also showed that the fold-change of VOCs from constitutive to induced state differed among individuals independently of the uniformity of the blends before herbivore attack. We discuss our findings in the context of the ecological roles of VOCs in plant-plant and plant-carnivore insects’ interactions.

Metal mobilization in soil by two structurally defined polyphenols

Polyphenols including tannins comprise a large percentage of plant detritus such as leaf litter, and affect soil processes including metal dynamics. We tested the effects of tannins on soil metal mobilization by determining the binding stoichiometries of two model polyphenols to Al(III) and Fe(III) using micelle-mediated separation and inductively coupled plasma optical emission spectroscopy (ICP-OES). By fitting the data to the Langmuir model we found the higher molecular weight polyphenol (oenothein B) was able to bind more metal than the smaller polyphenol (epigallocatechin gallate, EGCg). For example, oenothein B bound 9.43 mol Fe mol(-1), while EGCg bound 4.41 mol of Fe mol(-1). Using the parameters from the binding model, we applied the Langmuir model for competitive binding to predict binding for mixtures of Al(III) and Fe(III). Using the parameters from the single metal experiments and information about polyphenol sorption to soils we built a model to predict metal mobilization from soils amended with polyphenols. We tested the model with three natural soils and found that it predicted mobilization of Fe and Al with r(2)=0.92 and r(2)=0.88, respectively. The amount of metal that was mobilized was directly proportional to the maximum amount of metal bound to the polyphenol. The secondary parameter in each model was the amount of weak organically chelated Fe or Al that was in the soil. This study provides the first compound-specific information about how natural polyphenols interact with metals in the environment. We propose a model that is applicable to developing phytochelation agents for metal detoxification, and we discuss how tannins may play a role in metal mobilization from soils.

Qualitative variation in proanthocyanidin composition of Populus species and hybrids: genetics is the key

The literature on proanthocyanidins (tannins) in ecological systems is dominated by quantitative studies. Despite evidence that the qualitative characteristics (subunit type, polymer chain length) of these complex polyphenolics are important determinants of biological activity, little is known about genetic and environmental controls on the type of proanthocyanidins produced by plants. We tested the hypothesis that genetics, season, developmental stage, and environment determine proanthocyanidin qualitative characteristics by using four Populus "cross types" (narrowleaf [P. angustifolia], Fremont [P. fremontii], F1 hybrids, and backcrosses to narrowleaf). We used thiolysis and HPLC analysis to characterize the proanthocyanidins, and found that genetics strongly control composition. The narrowleaf plants accumulate mixed procyanidin/prodelphinidins with average composition epicatechin(11)-epigallocatechin(8)-catechin(2)-catechin((terminal)). Backcross genotypes produce mixed procyanidin/prodelphinidins similar to narrowleaf, while Fremont makes procyanidin dimers, and the F1 plants contain procyanidin heptamers. Less striking effects were noted for genotype × environment, while season and developmental zone had little effect on proanthocyanidin composition or chain length. We discuss the metabolic and ecological consequences of differences in condensed tannin qualitative traits.