Purification of archetypal soybean root suberin mostly comprising alka(e)noic acids using an ionic liquid catalyst

Soybean (Glycine max) is an increasingly relevant crop due to its economic importance and also a model plant for the study of root symbiotic associations with nodule forming rhizobia. Plant polyesters mediate plant-microbe interactions with both pathogenic and beneficial microbes; suberin has been hypothesized to play a key role during the early steps of rhizobia attachment to the root. The downside is that suberin chemistry in soybean root is still scarcely studied. This study addresses this outstanding question by reporting a straightforward workflow for a speedy purification of suberin from soybean root and for its subsequent detailed chemical analysis. To purify suberin, cholinium hexanoate (an ionic liquid) was used as the catalyst. The ensuing suberin is highly esterified as observed by a precise Nuclear Magnetic Resonance quantification of each ester type, discriminating between primary and acylglycerol esters. Moreover, the composing hydrolysable monomers detected through GC-MS revealed that hexadecanoic acid is the most abundant monomer, similar to that reported before by others. Overall, this study highlights the adequacy of the ionic liquid catalyst for the isolation of suberin from soybean roots, where the polymer natural abundance is low, and builds new knowledge on the specificities of its chemistry; essential to better understand the biological roles of suberin in roots.

Building Blocks of the Protective Suberin Plant Polymer Self-Assemble into Lamellar Structures with Antibacterial Potential

The protection of terrestrial plants from desiccation, mechanical injury, and pathogenic invasion is achieved by waxes and cutin polyesters on leaf and fruit surfaces as well as suberin polymers that are embedded in the cell walls of roots, but the physicochemical principles governing the organization of these biological composites remain incompletely understood. Despite the well-established enzymatic mediation of suberin formation in the skins of potato tubers, cork oak trees, and internal plant tissues, the additional possibility of self-assembly in this system was suggested by our serendipitous finding that solvent extracts from potato phellem tissues form suspended fibers and needles in the absence of such catalysts over a period of several weeks. In the current study, we investigated self-assembly for three-component model chemical mixtures comprised of a hydroxyfatty acid, glycerol, and either of two hydroxycinnamic acids that together typify the building blocks of potato suberin biopolymers. We demonstrate that these mixtures spontaneously form lamellar structures that are reminiscent of suberized plant tissues, incorporate all constituents into self-assemblies, can form covalently bound ester structures, and display antibacterial activity. These findings provide new perspectives on the self-association and reactivity of these classes of organic compounds, insights into agriculturally important suberin formation in food crops, and a starting point for engineering sustainable materials with antimicrobial capabilities.

Quantification of Structure-Property Relationships for Plant Polyesters Reveals Suberin and Cutin Idiosyncrasies

Polyesters, as they exist in planta, are promising materials with which to begin the development of "green" replacements. Cutin and suberin, polyesters found ubiquitously in plants, are prime candidates. Samples enriched for plant polyesters, and in which their native backbones were largely preserved, were studied to identify "natural" structural features; features that influence critical physical properties. Quantitative nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and X-ray scattering methods were used to quantify structure-property relationships in these polymeric materials. The degree of esterification, namely, the presence of acylglycerol linkages in suberin and of secondary esters in cutin, and the existence of mid-chain epoxide groups defining the packing of the aliphatic chains were observed. This packing determines polymer crystallinity, the resulting crystal structure, and the melting temperature. To evaluate the strength of this rule, tomato cutin from the same genotype, studying wild-type plants and two well-characterized mutants, was analyzed. The results show that cutin's material properties are influenced by the amount of unbound aliphatic hydroxyl groups and by the length of the aliphatic chain. Collectively, the acquired data can be used as a tool to guide the selection of plant polyesters with precise structural features, and hence physicochemical properties.

Implication of Threonine-Based Ionic Liquids on the Structural Stability, Binding and Activity of Cytochrome c

Ionic liquids (ILs) are useful in pharmaceutical industries and biotechnology as alternative solvents or sources for protein extraction and purification, preservation of biomolecules and for regulating the catalytic activity of enzymes. However, the binding mechanism, the non-covalent forces responsible for protein-IL interactions and dynamics of proteins in IL need to be investigated in depth for the effective use of ILs as alternatives. Herein, we disclose the molecular level understanding of the structural intactness and reactivity of a model protein cytochrome c (Cyt c) in biocompatible threonine-based ILs with the help of experimental techniques such as isothermal titration calorimetry (ITC), fluorescence spectroscopy, transmission electron microscopy (TEM) as well as molecular docking. Hydrophobic and electrostatic forces are responsible for the structural and conformational integrity of Cyt c in IL. The ITC experiments revealed the Cyt c-IL binding free energies are in the range of 10-14 kJ/mol and the molecular docking studies demonstrated that ILs interact at the surfaces of Cyt c. The results look promising as the ILs used here are non-toxic and biocompatible, and thus may find potential applications in structural biology and biotechnology.

Choline [Amino Acid] Ionic Liquid/Water Mixtures: A Triple Effect for the Degradation of an Organophosphorus Pesticide

A series of ionic liquids (ILs) composed by choline (Ch) as a cation and different amino acids (AA) as anions and their respective aqueous mixtures were prepared using different [Ch][AA] contents in a range of 0.4-46 mol % IL. These solvents were used for the first time to achieve an eco-friendlier Paraoxon degradation. The results show that [Ch][AA]/water mixtures are an effective reaction medium to degrade Paraoxon, even when the IL content in the mixture is low (0.4 mol % IL) and without the need of an extra nucleophile. Both the kinetics and the degradation pathways of pesticides depend on the nature of the AA on [Ch][AA] and the amount of an IL present in the mixture. We have demonstrated that in those mixtures with a low amount of [Ch][AA], the hydrolysis reaction is the main pathway for Paraoxon degradation, showing a catalytic effect of the IL. However, as the percentage of [Ch][AA] increases in the mixture, the nucleophilic attack of [Ch][AA] is evident. Finally, the aim of this study was to provide evidence of a promising and biocompatible methodology to degrade a toxic compound (Paraoxon) using a minimal quantity of an IL designed totally from natural resources.

Sustainable plant polyesters as substrates for optical gas sensors

The fast and non-invasive detection of odors and volatile organic compounds (VOCs) by gas sensors and electronic noses is a growing field of interest, mostly due to a large scope of potential applications. Additional drivers for the expansion of the field include the development of alternative and sustainable sensing materials. The discovery that isolated cross-linked polymeric structures of suberin spontaneously self-assemble as a film inspired us to develop new sensing composite materials consisting of suberin and a liquid crystal (LC). Due to their stimuli-responsive and optically active nature, liquid crystals are interesting probes in gas sensing. Herein, we report the isolation and the chemical characterization of two suberin types (from cork and from potato peels) resorting to analyses of gas chromatography–mass spectrometry (GC-MS), solution nuclear magnetic resonance (NMR), and X-ray photoelectron spectroscopy (XPS). The collected data highlighted their compositional and structural differences. Cork suberin showed a higher proportion of longer aliphatic constituents and is more esterified than potato suberin. Accordingly, when casted it formed films with larger surface irregularities and a higher C/O ratio. When either type of suberin was combined with the liquid crystal 5CB, the ensuing hybrid materials showed distinctive morphological and sensing properties towards a set of 12 VOCs (comprising heptane, hexane, chloroform, toluene, dichlormethane, diethylether, ethyl acetate, acetonitrile, acetone, ethanol, methanol, and acetic acid). The optical responses generated by the materials are reversible and reproducible, showing stability for 3 weeks. The individual VOC-sensing responses of the two hybrid materials are discussed taking as basis the chemistry of each suberin type. A support vector machines (SVM) algorithm based on the features of the optical responses was implemented to assess the VOC identification ability of the materials, revealing that the two distinct suberin-based sensors complement each other, since they selectively identify distinct VOCs or VOC groups. It is expected that such new environmentally-friendly gas sensing materials derived from natural diversity can be combined in arrays to enlarge selectivity and sensing capacity.

The molecular structure and multifunctionality of the cryptic plant polymer suberin

Suberin, a plant polyester, consists of polyfunctional long-chain fatty acids and glycerol and is an intriguing candidate as a novel antimicrobial material. We purified suberin from cork using ionic-liquid catalysis during which the glycerol bonds that ensure the polymeric nature of suberin remained intact or were only partially cleaved—yielding the closest to a native configuration reported to date.

The chemistry of suberin, both in situ (in cryogenically ground cork) and ex situ (ionic-liquid extracted), was elucidated using high-resolution one- and two-dimensional solution-state NMR analyses. Centrifugation was used to isolate suberin particles of distinct densities and their monomeric composition, assembly, and bactericidal effect, inter alia, were assessed.

Analysis of the molecular structure of suberin revealed the relative abundance of linear aliphatic vs. acylglycerol esters, comprising all acylglycerol configurations and the amounts of total carbonyls (C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]>O), free acid end groups (COOH), OH aliphatics, and OH aromatics. Suberin centrifuged fractions revealed generic physiochemical properties and monomeric composition ​and self-assemble into polygonal structures that display distinct degrees of compactness when lyophilized. Suberin particles—suberinsomes—display bactericidal activity against major human pathogenic bacteria.

Fingerprinting the multifunctionality of complex (plant) polyesters such as suberin allows for the identification of novel polymer assemblies with significant value-added properties.

The Hydrophobicity of Lignocellulosic Fiber Network Can Be Enhanced with Suberin Fatty Acids

Suberin fatty acids were extracted from outer bark of Silver birch (Betula pendula Roth.) using an isopropanolic sodium hydroxide solution. Laboratory sheets composed of lignocellulosic fiber networks were prepared from unbleached and unrefined softwood kraft pulp and further impregnated with suberin fatty acid monomers and cured with maleic anhydride in ethanol solution. The treatment resulted in hydrophobic surfaces, in which the contact angles remained over 120 degrees during the entire measurement. The fiber network also retained its water vapor permeability and enhanced fiber–fiber bonding resulted in improved tensile strength of the sheets. Scanning electron microscopy (SEM) images revealed that the curing agent, together with suberin fatty acids, was evenly distributed on the fiber surfaces and smoothing occurred over the wrinkled microfibrillar structure. High concentrations of the curing agent resulted in globular structures containing betulinol derivates as revealed with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Also, the larger amount of suberin fatty acid monomers slightly impaired the optical properties of sheets.

Using Thermodynamics to Assess the Molecular Interactions of Tetrabutylphosphonium Carboxylate–Water Mixtures

Densities, ρ, viscosities, η, and enthalpies of mixing, , of binary [P4 4 4 4][CnCOO]–water mixtures (with n=1, 2 or 7) were determined at atmospheric pressure as a function of temperature. The excess, , apparent, , and partial, , molar volumes were deduced from experimental data, as well as fragilities, m*, and excess Gibbs free energies of activation of viscous flow, . exhibited predominantly negative deviation from ideality, with a minimum at approximately ~0.8 for all three systems, indicating strong hydrogen-bonding interactions. All three binary systems were found to be fragile, with [P4 4 4 4][C7COO] showing the smallest deviations in fragility with the addition of water. values of the systems were exothermic over the entire composition range, having the following trend: [P4 4 4 4][C2COO]>[P4 4 4 4][C7COO]>[P4 4 4 4][C1COO].

Long-term protein packaging in bio-ionic liquids: Improved catalytic activity and enhanced stability of cytochrome C against multiple stresses

There is a considerable interest in the use of structurally stable and catalytically active enzymes, such as cytochrome C (Cyt C), in the pharmaceutical and fine chemical industries. However, harsh process conditions, such as temperature, pH, and presence of organic solvents, are the major barriers to the effective use of enzymes in biocatalysis. Herein, we demonstrate the suitability of bio-based ionic liquids (ILs) formed by the cholinium cation and dicarboxylate-based anions as potential media for enzymes, in which remarkable enhanced activity and improved stability of Cyt C against multiple stresses were obtained. Among the several bio-ILs studied, an exceptionally high catalytic activity (> 50-fold) of Cyt C was observed in aqueous solutions of cholinium glutarate ([Ch][Glu]; 1g/mL) as compared to the commonly used phosphate buffer solutions (pH 7.2), and > 25-fold as compared to aqueous solutions of cholinium dihydrogen phosphate ([Ch][Dhp]; 0.5g/mL) -the best known IL for long term stability of Cyt C. The catalytic activity of the enzyme in presence of bio-ILs was retained against several external stimulus, such as chemical denaturants (H2O2 and GuHCl), and temperatures up to 120 °C. The observed enzyme activity is in agreement with its structural stability, as confirmed by UV-Vis, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopies. Taking advantage of the multi-ionization states of di/tri-carboxylic acids, the pH was switched from acidic to basic by the addition of the corresponding carboxylic acid and choline hydroxide, respectively. The activity was found to be maximum at a 1:1 ratio of [Ch][carboxylate], with a pH in the range from 3 to 5.5. Moreover, it was found that the bio-ILs studied herein protect the enzyme against protease digestion and allow long-term storage (at least for 21 weeks) at room temperature. An attempt by molecular docking was also made to better understand the efficacy of the investigated bio-ILs towards the enhanced activity and long term stability of Cyt C. The results showed that dicarboxylates anions interact with the active site's amino acids of the enzyme through H-bonding and electrostatic interactions, which are responsible for the observed enhancement of the catalytic activity. Finally, it is demonstrated that Cyt C can be successfully recovered from the aqueous solution of bio-ILs and reused without compromising its yield, structural integrity and catalytic activity, thereby overcoming the major limitations in the use of IL-protein systems in biocatalysis.

Effect of Different Pretreatment Methods on Birch Outer Bark: New Biorefinery Routes

A comparative study among different pretreatment methods used for the fractionation of the birch outer bark components, including steam explosion, hydrothermal and organosolv treatments based on the use of ethanol/water media, is reported. The residual solid fractions have been characterized by ATR-FTIR, ¹³C-solid-state NMR and morphological alterations after pretreatment were detected by scanning electron microscopy. The general chemical composition of the untreated and treated bark including determination of extractives, suberin, lignin and monosaccharides was also studied. Composition of the residual solid fraction and relative proportions of different components, as a function of the processing conditions, could be established. Organosolv treatment produces a suberin-rich solid fraction, while during hydrothermal and steam explosion treatment cleavage of polysaccharide bonds occurs. This work will provide a deeper fundamental knowledge of the bark chemical composition, thus increasing the utilization efficiency of birch outer bark and may create possibilities to up-scale the fractionation processes.

Ionic Liquids as Unforeseen Assets to Fight Life-Threatening Mycotic Diseases

Ionic liquids discovery has celebrated 100 years. They consist solely of ions, one of which is typically organic and asymmetrical. Remarkable physical and chemical properties stirred their use as alternative solvents in many chemical processes. The recent demonstration of their occurrence in nature might boost their interest in biological sciences. In the search of mechanistic understandings of ionic liquids’ ecotoxicological impacts in fungi, we have analyzed the proteome, transcriptome, and metabolome responses to this chemical stress. Data illuminated new hypotheses that altered our research path – exploit ionic liquids as tools for the discovery of pathways and metabolites that may impact fungal development and pathogenicity. As we get closer to solve the primary effects of each ionic liquid family and their specific gene targets, the vision of developing antifungal ionic liquids and/or materials, by taking advantage of elegant progresses in this field, might become a reality. Task-designed formulations may improve the performance of conventional antifungal drugs, build functional coatings for reducing allergens production, or aid in the recovery of antifungal plant polymers. The frontier research in this cross-disciplinary field may provide us unforeseen means to address the global concern of mycotic diseases. Pathogenic and opportunistic fungi are responsible for numerous infections, killing annually nearly 1.5 million immunocompromised individuals worldwide, a similar rate to malaria or tuberculosis. This perspective will review our major findings and current hypotheses, contextualizing how they might bring us closer to efficient strategies to prevent and fight mycotic diseases.

Suberin: the biopolyester at the frontier of plants

Suberin is a lipophilic macromolecule found in specialized plant cell walls, wherever insulation or protection toward the surroundings is needed. Suberized cells form the periderm, the tissue that envelops secondary stems as part of the bark, and develop as the sealing tissue after wounding or leaf abscission. Suberin is a complex polyester built from poly-functional long-chain fatty acids (suberin acids) and glycerol. The suberin acids composition of a number of plant tissues and species is now established, but how the polyester macromolecule is assembled within the suberized cell walls is not known. In the last years contributions from several areas have however significantly enriched our understanding of suberin. The primary structure of the polyester, i.e., how the suberin acids and glycerol are sequentially linked was revealed, together with the stereochemistry of the mid-chain functional groups some suberin acids have; solid-state NMR studies showed the presence of methylene chains spatially separated and with different molecular mobility; biophysical studies showed the membrane behavior of suberin acids derivatives, allowing new insights on structure-properties relationships; and a number of candidate genes were conclusively related to suberin biosynthesis. The comprehension of suberin as a macromolecule will be essential to understand its vital protective roles in plants and how they will deal with eventual environmental changes. Suberin is also expected to be a source for high-performing bio-based chemicals, taking advantage of the structural uniqueness of their constituent suberin acids.

Impedance analysis of inherently redox-active ionic-liquid-based photoelectrochemical cells: charge-transfer mechanism in the presence of an additional redox couple

An intensive electrochemical impedance study was carried out to understand the charge-transfer processes in photoelectrochemical (PEC) cells based on ionic liquid (IL) electrolytes. Three different electrolytes were utilized to understand the role of redox species as well as the medium on the charge-transfer mechanism. The negligible diffusion resistance, despite the presence of two different redox species in the case of Fe(CN)(6) (-4/-3) in IL, was explained on the basis of charge transfer between species of two different redox couples. Accordingly, the redox species are not required to travel through the bulk of the electrolyte for the removal of accumulated charges, as short-range charge transfer between the IL and the Fe(CN)(6) (-4/-3) species facilitates the removal of accumulated charges. It is also shown that PEC cells utilizing dual redox couples are highly stable with larger photoelectrochmeical windows, >3 V.

An ionic liquid promoted microwave-hydrothermal route towards highly photoluminescent carbon dots for sensitive and selective detection of iron(iii)

Carbon dots with a high photoluminescence efficiency of ∼22.58% are obtained by a facile microwave-hydrothermal treatment of rice straw with the presence of ionic liquid.

Effect of choline carboxylate ionic liquids on biological membranes

Choline carboxylates, ChCm, with m=2-10 and choline oleate are known as biocompatible substances, yet their influence on biological membranes is not well-known, and the effect on human skin has not previously been investigated. The short chain choline carboxylates ChCm with m=2, 4, 6 act as hydrotropes, solubilizing hydrophobic compounds in aqueous solution, while the longer chain choline carboxylates ChCm with m=8, 10 and oleate are able to form micelles. In the present study, the cytotoxicity of choline carboxylates was tested using HeLa and SK-MEL-28 cells. The influence of these substances on liposomes prepared from dipalmitoylphosphatidylcholine (DPPC) was also evaluated to provide insights on membrane interactions. It was observed that the choline carboxylates with a chain length of m>8 distinctly influence the bilayer, while the shorter ones had minimal interaction with the liposomes.

Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source

BACKGROUND

Lipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both plant pathogenic and saprophytic fungi. Regardless of numerous reports on fungal degradation of emulsified fatty acids or cutin, and on fungi-plant interactions, the pathways involved in the degradation and utilisation of suberin remain largely overlooked. As a structural component of the plant cell wall, suberin isolation, in general, uses harsh depolymerisation methods that destroy its macromolecular structure. We recently overcame this limitation isolating suberin macromolecules in a near-native state.

RESULTS

Suberin macromolecules were used here to analyse the pathways involved in suberin degradation and utilisation by Aspergillus nidulans. Whole-genome profiling data revealed the complex degrading enzymatic machinery used by this saprophytic fungus. Initial suberin modification involved ester hydrolysis and ω-hydroxy fatty acid oxidation that released long chain fatty acids. These fatty acids were processed through peroxisomal β-oxidation, leading to up-regulation of genes encoding the major enzymes of these pathways (e.g. faaB and aoxA). The obtained transcriptome data was further complemented by secretome, microscopic and spectroscopic analyses.

CONCLUSIONS

Data support that during fungal growth on suberin, cutinase 1 and some lipases (e.g. AN8046) acted as the major suberin degrading enzymes (regulated by FarA and possibly by some unknown regulatory elements). Suberin also induced the onset of sexual development and the boost of secondary metabolism.