The macromolecular aromatic domain in suberized tissue: a changing paradigm

The Tomato Feruloyl Transferase FHT Promoter Is an Accurate Identifier of Early Development and Stress-Induced Suberization

As a wall polymer, suberin has a multifaceted role in plant development and stress responses. It is deposited between the plasma membrane and the primary cell wall in specialized tissues such as root exodermis, endodermis, phellem, and seed coats. It is formed de novo in response to stresses such as wounding, salt injury, drought, and pathogen attack and is a complex polyester mainly consisting of fatty acids, glycerol, and minor amounts of ferulic acid that are associated to a lignin-like polymer predominantly composed of ferulates. Metabolomic and transcriptomic studies have revealed that cell wall lignification precedes suberin deposition. The ferulic acid esterified to ω-hydroxy fatty acids, synthetized by the feruloyl transferase FHT (or ASFT), presumably plays a role in coupling both polymers, although the precise mechanism is not understood. Here, we use the promoter of tomato suberin feruloyl transferase (FHT/ASFT) fused to GUS (β-glucuronidase) to demonstrate that ferulate deposition agrees with the site of promoter FHT activation by using a combination of histochemical staining and UV microscopy. Hence, FHT promoter activation and alkali UV microscopy can be used to identify the precise localization of early suberizing cells rich in ferulic acid and can additionally be used as an efficient marker of early suberization events during plant development and stress responses. This line can be used in the future as a tool to identify emerging suberization sites via ferulate deposition in tomato plants, which may contribute to germplasm screening in varietal improvement programs.

Analytical Method Cluster Development for Comprehensive Characterisation of Suberinic Acids Derived from Birch Outer Bark

Suberin is a complex polyester biopolymer, and it is practically impossible to estimate the real content of suberin in suberised plant tissues. This indicates the importance of the development of instrumental analytical methods for the comprehensive characterisation of suberin derived from plant biomass for the successful integration of suberinic products into biorefinery production chains. In this study, we optimised two GC-MS methods-one with direct sylilation, and the second with additional depolymerisation, using GPC methods with RI detector and polystyrene calibration and with a three-angle light scattering detector and an eighteen-angle light scattering detector. We also performed MALDI-Tof analysis for non-degraded suberin structure determination. We characterised suberinic acid (SA) samples obtained from birch outer bark after alkaline depolymerisation. The samples were particularly rich in diols, fatty acids and their esters, hydroxyacids and their corresponding esters, diacids and their corresponding esters, as well as extracts (mainly betulin and lupeol) and carbohydrates. To remove phenolic-type admixtures, treatment with ferric chloride (FeCl₃) was used. The SA treatment with FeCl₃ allows the possibility to obtain a sample that has a lower content of phenolic-type compounds and a lower molecular weight than an untreated sample. It was possible to identify the main free monomeric units of SA samples by GC-MS system using direct silylation. By performing an additional depolymerisation step before silylation, it was possible to characterise the complete potential monomeric unit composition in the suberin sample. For the molar mass distribution determination, it is important to perform GPC analysis. Even though chromatographic results can be obtained using a three- laser MALS detector, they are not fully correct because of the fluorescence of the SA samples. Therefore an 18-angle MALS detector with filters was more suitable for SA analysis. MALDI-Tof analysis is a great tool for the polymeric compound structural identification, which cannot be done using GC-MS. Using the MALDI data, we discovered that the main monomeric units that makes up the SA macromolecular structure are octadecanedioic acid and 2-(1,3-dihydroxyprop-2-oxy)decanedioic acid. This corresponds with GC-MS results, showing that after depolymerisation hydroxyacids and diacids were the dominant type of compounds found in the sample.

An ABA-serotonin module regulates root suberization and salinity tolerance

Suberin in roots acts as a physical barrier preventing water/mineral losses. In Arabidopsis, root suberization is regulated by abscisic acid (ABA) and ethylene in response to nutrient stresses. ABA also mediates coordination between microbiota and root endodermis in mineral nutrient homeostasis. However, it is not known whether this regulatory system is common to plants in general, and whether there are other key molecule(s) involved. We show that serotonin acts downstream of ABA in regulating suberization in rice and Arabidopsis and negatively regulates suberization in rice roots in response to salinity. We show that ABA represses transcription of the key gene (OsT5H) in serotonin biosynthesis, thus promoting root suberization in rice. Conversely, overexpression of OsT5H or supplementation with exogenous serotonin represses suberization and reduces tolerance to salt stress. These results identify an ABA-serotonin regulatory module controlling root suberization in rice and Arabidopsis, which is likely to represent a general mechanism as ABA and serotonin are ubiquitous in plants. These findings are of significant importance to breeding novel crop varieties that are resilient to abiotic stresses and developing strategies for production of suberin-rich roots to sequestrate more CO₂ , helping to mitigate the effects of climate change.

Potato Periderm Development and Tuber Skin Quality

The periderm is a corky tissue that replaces the epidermis when the latter is damaged, and is critical for preventing pathogen invasion and water loss. The periderm is formed through the meristematic activity of phellogen cells (cork cambium). The potato skin (phellem cells) composes the outer layers of the tuber periderm and is a model for studying cork development. Early in tuber development and following tuber expansion, the phellogen becomes active and produces the skin. New skin layers are continuously added by division of the phellogen cells until tuber maturation. Some physiological disorders of the potato tuber are related to abnormal development of the skin, including skinning injuries and russeting of smooth-skinned potatoes. Thus, characterizing the potato periderm contributes to modeling cork development in plants and helps to resolve critical agricultural problems. Here, we summarize the data available on potato periderm formation, highlighting tissue characteristics rather than the suberization processes.

Induced ligno-suberin vascular coating and tyramine-derived hydroxycinnamic acid amides restrict Ralstonia solanacearum colonization in resistant tomato

Tomato varieties resistant to the bacterial wilt pathogen Ralstonia solanacearum have the ability to restrict bacterial movement in the plant. Inducible vascular cell wall reinforcements seem to play a key role in confining R. solanacearum into the xylem vasculature of resistant tomato. However, the type of compounds involved in such vascular physico-chemical barriers remain understudied, while being a key component of resistance. Here we use a combination of histological and live-imaging techniques, together with spectroscopy and gene expression analysis to understand the nature of R. solanacearum-induced formation of vascular coatings in resistant tomato. We describe that resistant tomato specifically responds to infection by assembling a vascular structural barrier formed by a ligno-suberin coating and tyramine-derived hydroxycinnamic acid amides. Further, we show that overexpressing genes of the ligno-suberin pathway in a commercial susceptible variety of tomato restricts R. solanacearum movement inside the plant and slows disease progression, enhancing resistance to the pathogen. We propose that the induced barrier in resistant plants does not only restrict the movement of the pathogen, but may also prevent cell wall degradation by the pathogen and confer anti-microbial properties, effectively contributing to resistance.

Suberin Biosynthesis, Assembly, and Regulation

Suberin is a specialized cell wall modifying polymer comprising both phenolic-derived and fatty acid-derived monomers, which is deposited in below-ground dermal tissues (epidermis, endodermis, periderm) and above-ground periderm (i.e., bark). Suberized cells are largely impermeable to water and provide a critical protective layer preventing water loss and pathogen infection. The deposition of suberin is part of the skin maturation process of important tuber crops such as potato and can affect storage longevity. Historically, the term "suberin" has been used to describe a polyester of largely aliphatic monomers (fatty acids, ω-hydroxy fatty acids, α,ω-dioic acids, 1-alkanols), hydroxycinnamic acids, and glycerol. However, exhaustive alkaline hydrolysis, which removes esterified aliphatics and phenolics from suberized tissue, reveals a core poly(phenolic) macromolecule, the depolymerization of which yields phenolics not found in the aliphatic polyester. Time course analysis of suberin deposition, at both the transcriptional and metabolite levels, supports a temporal regulation of suberin deposition, with phenolics being polymerized into a poly(phenolic) domain in advance of the bulk of the poly(aliphatics) that characterize suberized cells. In the present review, we summarize the literature describing suberin monomer biosynthesis and speculate on aspects of suberin assembly. In addition, we highlight recent advances in our understanding of how suberization may be regulated, including at the phytohormone, transcription factor, and protein scaffold levels.

Abscisic acid stimulates wound suberisation in kiwifruit (Actinidia chinensis) by regulating the production of jasmonic acid, cytokinin and auxin

Wounding induces a cascade of correlative physiological responses that lead to the repair of damaged tissue. In this study, the effect of wounding on suberin, endogenous hormones and their metabolic genes expression was observed during the wound healing of kiwifruit (Actinidia chinensis Planch.). In addition, the role of abscisic acid (ABA) in wound suberisation was investigated by analysing the coordinated regulation between ABA and other hormones. The wound healing process in kiwifruit could be divided into two stages including: (1) initial accumulation of suberin polyphenolic (SPP) and long carbon chain suberin polyaliphatic monomers (LSPA) before 24h; and (2) massive synthesis of SPP and very long carbon chain suberin polyaliphatic monomers (VLSPA) after 24h. ABA content rapidly increased and induced the jasmonic acid (JA) biosynthesis at the early stage of wound healing. ABA level gradually decreased with the expression of AchCYP707A genes, while the contents of trans-zeatin (t-ZT) and indole-3-acetic acid (IAA) steadily increased at the late stage of wound healing. Exogenous ABA stimulated JA and suberin monomers accumulation, but suppressed both t-ZT and IAA biosynthesis. The role of ABA in wound healing of kiwifruit might be involved in the coordination of both JA-mediated suberin monomers biosynthesis and t-ZT- and IAA-mediated formation of suberised cells via an interaction mechanism.

Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria

Root-knot nematodes (RKNs) are among the most devastating pests in agriculture. Solanum torvum Sw. (Turkey berry) has been used as a rootstock for eggplant (aubergine) cultivation because of its resistance to RKNs, including Meloidogyne incognita and M. arenaria. We previously found that a pathotype of M. arenaria, A2-J, is able to infect and propagate in S. torvum. In vitro infection assays showed that S. torvum induced the accumulation of brown pigments during avirulent pathotype A2-O infection, but not during virulent A2-J infection. This experimental system is advantageous because resistant and susceptible responses can be distinguished within a few days, and because a single plant genome can yield information about both resistant and susceptible responses. Comparative RNA-sequencing analysis of S. torvum inoculated with A2-J and A2-O at early stages of infection was used to parse the specific resistance and susceptible responses. Infection with A2-J did not induce statistically significant changes in gene expression within one day post-inoculation (DPI), but afterward, A2-J specifically induced the expression of chalcone synthase, spermidine synthase, and genes related to cell wall modification and transmembrane transport. Infection with A2-O rapidly induced the expression of genes encoding class III peroxidases, sesquiterpene synthases, and fatty acid desaturases at 1 DPI, followed by genes involved in defense, hormone signaling, and the biosynthesis of lignin at 3 DPI. Both isolates induced the expression of suberin biosynthetic genes, which may be triggered by wounding during nematode infection. Histochemical analysis revealed that A2-O, but not A2-J, induced lignin accumulation at the root tip, suggesting that physical reinforcement of cell walls with lignin is an important defense response against nematodes. The S. torvum-RKN system can provide a molecular basis for understanding plant-nematode interactions.

RNAi Modulation of Chlorogenic Acid and Lignin Deposition in Nicotiana tabacum and Insufficient Compensatory Metabolic Cross-Talk

Chlorogenic acid (CGA) and guaiacyl/syringyl (G/S) lignin formation involves hydroxycinnamoyl ester intermediacy, the latter formed via hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT) and hydroxycinnamoyl CoA:quinate hydroxycinnamoyl transferase (HQT) activities. HQT and HCT RNAi silencing of a commercial tobacco (Nicotiana tabacum) K326 line was examined herein. NtHQT gene silencing gave relatively normal plant phenotypes, with CGA levels reduced (down to 1% of wild type) with no effects on lignin. RNAi NtHCT silencing had markedly adverse phenotypes (e.g., stunted, multiple stems, delayed flowering, with senescence delayed by several months). Lignin contents were partially lowered, with a small increase in cleavable p-hydroxyphenyl (H) monomers; those plants had no detectable CGA level differences relative to wild type. In vitro NtHCT kinetic parameters revealed preferential p-coumaroyl CoA and shikimate esterification, as compared to other structurally related potential acyl group donors and acceptors. In the presence of coenzyme A, NtHCT catalyzed the reverse reaction. Site-directed mutagenesis of NtHCT (His153Ala) abolished enzymatic activity. NtHQT, by comparison, catalyzed preferential conversion of p-coumaroyl CoA and quinic acid to form p-coumaroyl quinate, the presumed CGA precursor. In sum, metabolic pathways to CGA and lignins appear to be fully independent, and previous conflicting reports of substrate versatilities and metabolic cross-talk are resolved.

Importance of suberin biopolymer in plant function, contributions to soil organic carbon and in the production of bio-derived energy and materials

Suberin is a hydrophobic biopolymer of significance in the production of biomass-derived materials and in biogeochemical cycling in terrestrial ecosystems. Here, we describe suberin structure and biosynthesis, and its importance in biological (i.e., plant bark and roots), ecological (soil organic carbon) and economic (biomass conversion to bioproducts) contexts. Furthermore, we highlight the genomics and analytical approaches currently available and explore opportunities for future technologies to study suberin in quantitative and/or high-throughput platforms in bioenergy crops. A greater understanding of suberin structure and production in lignocellulosic biomass can be leveraged to improve representation in life cycle analysis and techno-economic analysis models and enable performance improvements in plant biosystems as well as informed crop system management to achieve economic and environmental co-benefits.

Synthesis of 13 C-labelled cutin and suberin monomeric dicarboxylic acids of the general formula HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28)

13 C-labeled dicarboxylic acids HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28) have been synthesized as internal standards for LC-MS and GC-MS analysis of cutin and suberin monomer degradation by soil-based microorganisms. Different synthetic strategies had to be applied depending on the chain length of the respective synthetic target and because of economic considerations. 13 C-labels were introduced by nucleophilic substitution of a suitable leaving group with labelled potassium cyanide and subsequent hydrolysis of the nitriles to produce the corresponding dicarboxylic acids. All new compounds are characterized by GC/MS, IR, and NMR methods as well as by elemental analysis.

Bioinspired All-Polyester Diblock Copolymers Made from Poly(pentadecalactone) and Poly(2-(2-hydroxyethoxy)benzoate): Synthesis and Polymer Film Properties

The bioinspired diblock copolymers poly(pentadecalactone)-block-poly(2-(2-hydroxyethoxy)-benzoate) (PPDL-block-P2HEB) were synthesized from pentadecalactone and dihydro-5H-1,4-benzodioxepin-5-one (2,3-DHB). No transesterification between the blocks was observed. In a sequential approach, PPDL obtained by ring-opening polymerization (ROP) was used to initiate 2,3-DHB. Here, the molar mass Mn of the P2HEB block was limited. In a modular approach, end-functionalized PPDL and P2HEB were obtained separately by ROP with functional initiators, and connected by 1,3-dipolar Huisgen reaction ("click-chemistry"). Block copolymer compositions from 85:15 mass percent to 28:72 mass percent (PPDL:P2HEB) were synthesized, with Mn of from about 30,000-50,000 g mol-1. The structure of the block copolymer was confirmed by proton NMR, FTIR spectroscopy, and gel permeation chromatography. Morphological studies by atomic force microscopy (AFM) further confirmed the block copolymer structure, while quantitative nanomechanical AFM measurements revealed that the DMT moduli of the block copolymers ranged between 17.2 ± 1.8 MPa and 62.3 ± 5.7 MPa, i.e. between the values of the parent P2HEB and PPDL homopolymers (7.6 ± 1.4 MPa and 801 ± 42 MPa, respectively). Differential scanning calorimetry showed that the thermal properties of the homopolymers were retained by each of the copolymer blocks (melting temperature 90 °C, glass transition temperature 36 °C).

Bioinspired All-Polyester Diblock Copolymers Made from Poly(pentadecalactone) and Poly(3-hydroxycinnamate): Synthesis and Polymer Film Properties

A bioinspired diblock copolymer was synthesized from pentadecalactone and 3-hydroxy cinnamic acid. Poly(pentadecalactone) (PPDL) with a molar mass of up to 43,000 g mol-1 was obtained by ring-opening polymerization initiated propargyl alcohol. Poly(3-hydroxy cinnamate) (P3HCA) was obtained by polycondensation and end-functionalized with 3-azido propanol. The two functionalized homopolymers were connected via 1,3-dipolar Huisgen addition to yield the block copolymer PPDL-triazole-P3HCA. The structure the block copolymer was confirmed by proton NMR, FTIR spectroscopy and GPC. By analyzing the morphology of polymer films made from the homopolymers, from a 1:1 homopolymer blend, and from the PPDL-triazole-P3HCA block copolymer, clearly distinct micro- and nanostructures were revealed. Quantitative nanomechanical measurements revealed that the block copolymer PPDL-triazole-P3HCA had a DMT modulus of 22.3 ± 2.7 MPa, which was lower than that of the PPDL homopolymer (801 ± 42 MPa), yet significantly higher than that of the P3HCA homopolymer (1.77 ± 0.63 MPa). Thermal analytics showed that the melting point of PPDL-triazole-P3HCA was similar to PPDL (89-90 °C), while it had a glass transition was similar to P3HCA (123-124 °C). Thus, the semicrystalline, potentially degradable all-polyester block copolymer PPDL-triazole-P3HCA combines the thermal properties of either homopolymer, and has an intermediate elastic modulus.

Enzymatic Degradation of p-Nitrophenyl Esters, Polyethylene Terephthalate, Cutin, and Suberin by Sub1, a Suberinase Encoded by the Plant Pathogen Streptomyces scabies

The genome of Streptomyces scabies, the predominant causal agent of potato common scab, encodes a potential cutinase, the protein Sub1, which was previously shown to be specifically induced in the presence of suberin. The sub1 gene was expressed in Escherichia coli and the recombinant protein Sub1 was purified and characterized. The enzyme was shown to be versatile because it hydrolyzes a number of natural and synthetic substrates. Sub1 hydrolyzed p-nitrophenyl esters, with the hydrolysis of those harboring short carbon chains being the most effective. The V_max and K_m values of Sub1 for p-nitrophenyl butyrate were 2.36 mol g^-1 min^-1 and 5.7 10^-4 M, respectively. Sub1 hydrolyzed the recalcitrant polymers cutin and suberin because the release of fatty acids from these substrates was observed following the incubation of the enzyme with these polymers. Furthermore, the hydrolyzing activity of the esterase Sub1 on the synthetic polymer polyethylene terephthalate (PET) was demonstrated by the release of terephthalic acid (TA). Sub1 activity on PET was markedly enhanced by the addition of Triton and was shown to be stable at 37°C for at least 20 d.

The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway

The outer potato periderm layer consists of dead suberized cells. Suberin, a protective biopolymer, is made of a polyaliphatic portion covalently linked to polyaromatic moieties. Evidence accumulates that Streptomyces scabies, the main causal agent of potato common scab, can degrade the suberin aliphatic part but its ability to degrade the aromatic portion has not been documented. This polyaromatic portion is mainly composed of cinnamic acids. In this study, two cinnamates (trans-ferulic or p-coumaric acids) were added to the culture medium of S. scabies strains EF-35 and 87.22. HPLC quantification revealed that both strains efficiently utilized these compounds. A proteomic study coupled with gene expression analysis led to the identification of putative catabolic pathways for cinnamates. Catabolism of both compounds appeared to occur via the β-ketoadipate pathway. Gene SCAB_15301, encoding for a putative vanillate monooxygenase, was partly deleted from S. scabies strain 87.22 genome. The mutant retained its ability to catabolize trans-ferulic acid into vanillate but lost its ability to further degrade the latter compound. When the wild-type mutant and complemented strains were grown in the presence of suberin-enriched potato periderm, accumulation of vanillic acid was observed only in the mutant culture medium. This work presents evidence that S. scabies can degrade not only the aliphatic part of suberin but also the constituents of suberin aromatic portion. This may provide ecological and pathological advantages to S. scabies as a saprophyte and pathogen.

Effects of Polyhalite Fertilization on Skin Quality of Potato Tuber

The protective peel of potato tuber consists of periderm tissue, the outmost cell layers of which contain corky cell walls and are termed "skin". The skin protects the tuber from water loss and pathogen invasion, and its visual appearance is a highly important marketing factor. Physiological skin blemishes are of great concern, mainly russeting disorder and skinning injuries. We previously showed that application of calcium (Ca) reduces the rate and severity of skin russeting. Here, polyhalite fertilization was tested as an alternative source of Ca. The polyhalite mineral is a hydrated sulfate of potassium (K), Ca, and magnesium (Mg), and thus contains additional important nutrients that may contribute to skin quality. Furthermore, in view of the direct interaction of soil mineral elements with the tuber skin, we tested application of polyhalite at the end of the growth period, assuming that providing the mineral at the last stages of skin development may enhance its quality. Accordingly, polyhalite was applied at three time points: preplanting, in-season at around 3-4 weeks prior to haulm desiccation, and 2 days post-haulm desiccation. The experiments included several cultivars and locations. Data indicated that late application of polyhalite, after haulm desiccation, results in reduced concentrations of Ca and Mg and increased concentration of K in the tuber peel of fertilized plants compared to controls. Tuber appearance was improved, and the expression of FHT and CYP86A33, indicator genes for skin suberization, was significantly upregulated. Earlier applications of the polyhalite mineral did not alter mineral elements concentrations in the tuber peel compared to control plants. Overall, polyhalite fertilization positively affected tuber skin appearance and skin-related gene expression. However, the effect was moderate, and the mineral did not fully mitigate skin imperfections. The effect of polyhalite may be dependent on local conditions and cultivar type.

Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues

The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.

Identification of genes related to skin development in potato

Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh. Several genes that were differentially expressed in the skin (as verified by qPCR) and had not been previously identified in potato were selected for further analysis. These included the StKCS20-like, StFAR3, StCYP86A22 and StPOD72-like genes, whose sequences suggest that they may be closely related to known suberin-related genes; the StHAP3 transcription factor that directs meristem-specific expression; and the StCASP1B2-like and StCASP1-like genes, which are two orthologs of a protein family that mediates the formation of Casparian strips in the suberized endodermis of Arabidopsis roots. An examination of microtubers induced from transgenic plants carrying GUS reporter constructs of these genes indicated that these genes were expressed in the skin, with little to no expression in the tuber flesh. Some of the reporter constructs were preferentially expressed in the inner layers of the skin, the root endodermis, the vascular cambium and the epidermis of the stem. Cis-regulatory elements within the respective promoter sequences support this gene-expression pattern.

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.

Chlorogenic Acid Biosynthesis Appears Linked with Suberin Production in Potato Tuber (Solanum tuberosum)

Potato (Solanum tuberosum L.) is a good source of dietary antioxidants. Chlorogenic acid (CGA) and caffeic acid (CA) are the most abundant phenolic acid antioxidants in potato and are formed by the phenylpropanoid pathway. A number of CGA biosynthetic routes that involve hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT) and/or hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) have been proposed, but little is known about their path in potato. CA production requires a caffeoyl shikimate esterase (CSE), and CA serves as a substrate of lignin precursor ferulic acid via the action of caffeic/5-hydroxyferulic acid O-methyltransferase (COMT I). CGA is precursor of caffeoyl-CoA and, via caffeoyl-CoA O-methyltransferase (CCoAOMT), of feruloyl-CoA. Feruloyl-CoA is required for lignin and suberin biosynthesis, crucial for tuber development. Here, metabolite and transcript levels of the mentioned and related enzymes, such as cinnamate 4-hydroxylase (C4H), were determined in the flesh and skin of fresh and stored tubers. Metabolite and transcript levels were higher in skin than in flesh, irrespective of storage. CGA and CA production appear to occur via p-coumaroyl-CoA, using HQT and CSE, respectively. HCT is likely involved in CGA remobilization toward suberin. The strong correlation between CGA and CA, the correspondence with C4H, HQT, CCoAOMT2, and CSE, and the negative correlation of HCT and COMT I in potato tubers suggest a major flux toward suberin.

Role of HXXXD-motif/BAHD acyltransferases in the biosynthesis of extracellular lipids

Terrestrial plants have evolved specific adaptations to preserve water and protect themselves from their environment. Such adaptations range from secondary metabolites and specialized structures that conduct water and nutrients, to cell wall modifications (i.e., cuticle and suberin) that prevent dehydration and provide a physical barrier to pathogens. Both the plant cuticle and suberized cell walls contain a lipid polymer framework embedded with waxes, and constitute a promising target for controlled genetic modification to improve desirable agronomic traits. Recent advances in genomic and molecular techniques coupled with the development of robust analytical methods have accelerated progress in comprehending these intractable lipid polymers. Gene products characterized in the wax, cutin and suberin pathways include a subset of HXXXD/BAHD family enzymes that catalyze acyl transfer reactions between CoA-activated hydroxycinnamic acid derivatives and hydroxylated aliphatics. This review highlights our current understanding of HXXXD/BAHD acyltransferases in extracellular lipid biosynthesis and discusses the chemical, ultrastructural and physiological ramifications of impairing the expression of BAHD acyltransferase-encoding genes related to cutin and suberin synthesis.

Apoplastic barrier development and water transport in Zea mays seedling roots under salt and osmotic stresses

The development of apoplastic barriers was studied in Zea mays seedling roots grown in hydroculture solution supplemented with 0-200 mM NaCl or 20% polyethylene glycol (PEG). Casparian bands in the endodermis of both NaCl- and PEG-treated roots were observed closer to the root tip in comparison with those of control roots, but the cell wall modifications in the endodermis and exodermis induced by salt and osmotic stresses differed. High salinity induced the formation of a multiseriate exodermis, which ranged from several cell layers to the entire cortex tissue but did not noticeably influence cell wall suberization in the endodermis. In contrast, osmotic stress accelerated suberization in both the endodermis and exodermis, but the exodermis induced by osmotic stress was limited to several cell layers in the outer cortex adjacent to the epidermis. The hydrostatic hydraulic conductivity (Lp) had decreased significantly after 1 day of PEG treatment, whereas in NaCl-treated roots, Lp decreased to a similar level after 5 days of treatment. Peroxidase activity in the roots increased significantly in response to NaCl and PEG treatments. These data indicate that salt stress and osmotic stress have different effects on the development of apoplastic barriers and water transport in Z. mays seedling roots.

Kinetics of apple polyphenol diffusion in solutions with different osmotic strengths

Fruits contain polyphenols, widespread antioxidants beneficial for human health. Their mass transfer was studied during the leaching of apple slices immersed in mannitol solutions with ranging concentrations (0, 0.2, 0.4, and 0.6 M). The solution of Fick's law for unsteady mass transfer in planar configuration was used to calculate apparent diffusivity (De). Polyphenols were quantified by high-performance liquid chromatography for each immersion time. Leaching from raw apple tissues occurred only when cell integrity was lost, here at a certain level of difference in osmotic pressure. Different diffusivity values were found in the two apple varieties. Values of De either decreased from 0.2 to 0.1 × 10(-9) and 0.2 × 10(-9) m(2) s(-1) for Golden Delicious and Granny Smith, respectively, or were not determined when the mannitol concentration increased from 0 to 0.6 M. The osmotic strength of the solution strongly impacted the leaching rate of polyphenols from apple cells. The structure of the polyphenols also affected De, with low values for procyanidins.

Peroxidase activity in scutella of maize in association with anatomical changes during germination and grain storage

The embryo of the maize grain (Zea mays L.) is separated from the starchy endosperm by a fibrous structure, which is called the fibrous layer (FL). Using histochemical staining, it was determined that the FL is composed of collapsed cellular layers that contain phenols, neutral lipids, and 1,3-β-glucan. Due to its composition, the FL prevents free diffusion and separates the embryo from the endosperm during germination. Twenty-four hours after imbibition, the scutellum epidermis initiated a series of asynchronous spatial modifications, including cell growth, the perforation of cell walls, increased peroxidase activity in the apoplastic space, and elevated levels of superoxide, phenols, and other components that interact with the fibrous layer, enabling its transformation in addition to the free flow between compartments. During storage at high relative humidity levels, which leads to fast or slow deterioration depending on the temperature, the activity of phenol peroxidase in the scutellum was associated with a loss of vigor and reduced germination capacity when compared with low temperature and low relative humidity conditions. Such deterioration is associated with alterations in autofluorescent emissions from endogenous compounds in the scutellum, indicating changes in the microenvironment or in the differential proportions of epidermal and FL components.

Deconstructing a plant macromolecular assembly: chemical architecture, molecular flexibility, and mechanical performance of natural and engineered potato suberins

Periderms present in plant barks are essential protective barriers to water diffusion, mechanical breakdown, and pathogenic invasion. They consist of densely packed layers of dead cells with cell walls that are embedded with suberin. Understanding the interplay of molecular structure, dynamics, and biomechanics in these cell wall-associated insoluble amorphous polymeric assemblies presents substantial investigative challenges. We report solid-state NMR coordinated with FT-IR and tensile strength measurements for periderms from native and wound-healing potatoes and from potatoes with genetically modified suberins. The analyses include the intact suberin aromatic-aliphatic polymer and cell-wall polysaccharides, previously reported soluble depolymerized transmethylation products, and undegraded residues including suberan. Wound-healing suberized potato cell walls, which are 2 orders of magnitude more permeable to water than native periderms, display a strikingly enhanced hydrophilic-hydrophobic balance, a degradation-resistant aromatic domain, and flexibility suggestive of an altered supramolecular organization in the periderm. Suppression of ferulate ester formation in suberin and associated wax remodels the periderm with more flexible aliphatic chains and abundant aromatic constituents that can resist transesterification, attenuates cooperative hydroxyfatty acid motions, and produces a mechanically compromised and highly water-permeable periderm.

Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color

Sand pear (Pyrus pyrifolia) russet pericarp is an important trait affecting both the quality and stress tolerance of fruits. This trait is controlled by a relative complex genetic process, with some fundamental biological questions such as how many and which genes are involved in the process remaining elusive. In this study, we explored differentially expressed genes between the russet- and green-pericarp offspring from the sand pear (Pyrus pyrifolia) cv. 'Qingxiang' × 'Cuiguan' F1 group by RNA-seq-based bulked segregant analysis (BSA). A total of 29,100 unigenes were identified and 206 of which showed significant differences in expression level (log2fold values>1) between the two types of pericarp pools. Gene Ontology (GO) analyses detected 123 unigenes in GO terms related to 'cellular_component' and 'biological_process', suggesting developmental and growth differentiations between the two types. GO categories associated with various aspects of 'lipid metabolic processes', 'transport', 'response to stress', 'oxidation-reduction process' and more were enriched with genes with divergent expressions between the two libraries. Detailed examination of a selected set of these categories revealed repressed expressions of candidate genes for suberin, cutin and wax biosynthesis in the russet pericarps.Genes encoding putative cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD) that are involved in the lignin biosynthesis were suggested to be candidates for pigmentation of sand pear russet pericarps. Nine differentially expressed genes were analyzed for their expressions using qRT-PCR and the results were consistent with those obtained from Illumina RNA-sequencing. This study provides a comprehensive molecular biology insight into the sand pear pericarp pigmentation and appearance quality formation.

Investigating Aspergillus nidulans secretome during colonisation of cork cell walls

Cork, the outer bark of Quercus suber, shows a unique compositional structure, a set of remarkable properties, including high recalcitrance. Cork colonisation by Ascomycota remains largely overlooked. Herein, Aspergillus nidulans secretome on cork was analysed (2DE). Proteomic data were further complemented by microscopic (SEM) and spectroscopic (ATR-FTIR) evaluation of the colonised substrate and by targeted analysis of lignin degradation compounds (UPLC-HRMS). Data showed that the fungus formed an intricate network of hyphae around the cork cell walls, which enabled polysaccharides and lignin superficial degradation, but probably not of suberin. The degradation of polysaccharides was suggested by the identification of few polysaccharide degrading enzymes (β-glucosidases and endo-1,5-α-l-arabinosidase). Lignin degradation, which likely evolved throughout a Fenton-like mechanism relying on the activity of alcohol oxidases, was supported by the identification of small aromatic compounds (e.g. cinnamic acid and veratrylaldehyde) and of several putative high molecular weight lignin degradation products. In addition, cork recalcitrance was corroborated by the identification of several protein species which are associated with autolysis. Finally, stringent comparative proteomics revealed that A. nidulans colonisation of cork and wood share a common set of enzymatic mechanisms. However the higher polysaccharide accessibility in cork might explain the increase of β-glucosidase in cork secretome.

BIOLOGICAL SIGNIFICANCE

Cork degradation by fungi remains largely overlook. Herein we aimed at understanding how A. nidulans colonise cork cell walls and how this relates to wood colonisation. To address this, the protein species consistently present in the secretome were analysed, as well as major alterations occurring in the substrate, including lignin degradation compounds being released. The obtained data demonstrate that this fungus has superficially attacked the cork cell walls apparently by using both enzymatic and Fenton-like reactions. Only a few polysaccharide degrading enzymes could be detected in the secretome which was dominated by protein species associated with autolysis. Lignin degradation was corroborated by the identification of some degradation products, but the suberin barrier in the cell wall remained virtually intact. Comparative proteomics revealed that cork and wood colonisation share a common set of enzymatic mechanisms.

Characterization and ectopic expression of a populus hydroxyacid hydroxycinnamoyltransferase

Cutinized and suberized cell walls in plants constitute physiologically important environment interfaces. They act as barriers limiting the loss of water and nutrients and protecting against radiation and invasion of pathogens. The roles of cutin- and suberin polyesters are often attributed to their dominant aliphatic components, but the contribution of aromatic composition to their physiological function remains unclear. By functionally screening a subset of Populus trichocarpa BAHD/HXXXD acyltransferases, we identified a hydroxycinnamoyltransferase that shows specific transacylation activity on ω-hydroxyacids using both feruloyl- and p-coumaroyl- CoA as the acyl donors. We named this enzyme P. trichocarpa hydroxyacid/fatty alcohol hydroxycinnamoyltransferase 1 (PtFHT1). The ectopic expression of the PtFHT1 gene in Arabidopsis increased the incorporation of ferulate in root and seed suberins and in leaf cutin, but not that of p-coumarate, while the aliphatic load in both suberin and cutin polyesters essentially remained unaffected. The overaccumulation of ferulate in lipophilic polyester significantly increased the tolerance of transgenic plants to salt stress treatment; under sub-lethal conditions of salt stress, the ratios of their seed germination and seedling establishment were 50% higher than those of wild-type plants. Our study suggests that, although aromatics are the minor component of polyesters, they play important role in the sealing function of lipidic polymers in planta.

Oligomerization of 10,16-dihydroxyhexadecanoic acid and methyl 10,16-dihydroxyhexadecanoate catalyzed by lipases

The main monomer of tomato cuticle, 10,16-dihydroxyhexadecanoic acid (10,16-DHPA) and its methyl ester derivative (methyl-10,16-dihydroxyhexadecanote; methyl-10,16-DHHD), were used to study their oligomerization reactions catalyzed by five lipases: Candida antarctica lipase B (CAL-B), Rhizomucor miehei lipase (RM), Thermomyces lanuginosus lipase (TL), Pseudomonas cepacia lipase (PCL) and porcine pancreatic lipase (PPL). For 10,16-DHPA, optimum yields were obtained at 60 °C using toluene and 2-methyl-2-butanol (2M2B) as solvent, while for methyl-10,16-DHHD the bests yields were obtained in toluene and acetonitrile. Both reactions leaded to linear polyesters according to the NMR and FT-IR analysis, and there was no data indicating the presence of branched polymers. Using optimized conditions, poly(10,16-DHPA) and poly(methyl-10,16-DHHD) with Mw = 814 and Mn = 1,206 Da, and Mw = 982 and Mn = 860 Da, respectively, were formed according to their MALDI-TOF MS and ESI-MS data. The self-assembly of the polyesters obtained were analyzed by AFM.

Mini-review: what nuclear magnetic resonance can tell us about protective tissues

The epidermis and periderm protect plants from water and solute loss, pathogen invasion, and UV radiation. The cell walls of these protective tissues deposit the insoluble lipid biopolyesters cutin and suberin, respectively. These biopolymers interact in turn with polysaccharides, waxes and aromatic compounds to create complex assemblies that are not yet well defined at the molecular level. Non-destructive approaches must be tailored to the insoluble and noncrystalline character of these assemblies to establish the polymer and inter-component interactions needed to create functional barriers and structural supports. In the present mini-review, we illustrate the contribution of solid-state NMR methodology to compare the architecture of intact fruit cuticular polymers in wild-type and single-gene mutant tomatoes. We also show the potential of NMR-based metabolomics to identify the soluble metabolites that contribute to barrier formation in different varieties of potato tubers. Finally, we outline the challenges of these spectroscopic approaches, which include limited spectral resolution in solid state, differential swelling capabilities in solution, and incomplete dissolution in ionic liquids. Given the many genetically modified plants with altered suberin and cutin polymers that are now available, NMR nonetheless offers a promising tool to gain molecular insight into the complexity of these protective materials.

FT-ICR/MS and GC-EI/MS metabolomics networking unravels global potato sprout's responses to Rhizoctonia solani infection

The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents.

Upstream sequence of fatty acyl-CoA reductase (FAR6) of Arabidopsis thaliana drives wound-inducible and stem-specific expression

An Arabidopsis mutant line T90, exhibiting a stem-specific and wound-responsive GUS expression was identified from a population of Arabidopsis thaliana tagged with a promoterless β-glucuronidase (GUS) in the T-DNA. Sequence flanking the insertion from the right border was amplified by TAIL PCR and cloned. The insertion was located in the third chromosome, 57 bp upstream of the ATG start codon in 5' untranslated region (UTR) of the fatty acyl-CoA reductase 6 (FAR6) gene. RT-PCR analysis of the FAR6 gene revealed that the gene is expressed predominantly in stem tissue. Semi-quantitative RT-PCR showed that the expression is also induced by wounding in the epidermal layer of mature stem internodes. The transcription initiation site (TSS) was identified by 5' RACE PCR. Different 5' deletion fragments of the promoter sequences were developed and linked to the GUS reporter gene as transcriptional fusions and the expression patterns of GUS were histochemically analyzed in transgenic Arabidopsis plants. Sequences from -510 bp upstream to the transcriptional start site were sufficient to exhibit wound-inducible GUS expression in the stems. The addition of further upstream sequences (-510 to -958, -1,400 or -1,456) enhanced and extended the wound-inducible GUS expression throughout the mature stem.

Arogenate dehydratase isoenzymes profoundly and differentially modulate carbon flux into lignins

How carbon flux differentially occurs in vascular plants following photosynthesis for protein formation, phenylpropanoid metabolism (i.e. lignins), and other metabolic processes is not well understood. Our previous discovery/deduction that a six-membered arogenate dehydratase (ADT1-6) gene family encodes the final step in Phe biosynthesis in Arabidopsis thaliana raised the fascinating question whether individual ADT isoenzymes (or combinations thereof) differentially modulated carbon flux to lignins, proteins, etc. If so, unlike all other lignin pathway manipulations that target cell wall/cytosolic processes, this would be the first example of a plastid (chloroplast)-associated metabolic process influencing cell wall formation. Homozygous T-DNA insertion lines were thus obtained for five of the six ADTs and used to generate double, triple, and quadruple knockouts (KOs) in different combinations. The various mutants so obtained gave phenotypes with profound but distinct reductions in lignin amounts, encompassing a range spanning from near wild type levels to reductions of up to ∼68%. In the various KOs, there were also marked changes in guaiacyl:syringyl ratios ranging from ∼3:1 to 1:1, respectively; these changes were attributed to differential carbon flux into vascular bundles versus that into fiber cells. Laser microscope dissection/pyrolysis GC/MS, histochemical staining/lignin analyses, and pADT::GUS localization indicated that ADT5 preferentially affects carbon flux into the vascular bundles, whereas the adt3456 knock-out additionally greatly reduced carbon flux into fiber cells. This plastid-localized metabolic step can thus profoundly differentially affect carbon flux into lignins in distinct anatomical regions and provides incisive new insight into different factors affecting guaiacyl:syringyl ratios and lignin primary structure.

Derivatives of 10,16-dihydroxyhexadecanoic acid isolated from tomato (Solanum lycopersicum) as potential material for aliphatic polyesters

The main monomer of tomato cuticle, 10,16-dihydroxyhexadecanoic acid (or 10,16-dihydroxypalmitic acid; 10,16-DHPA), was isolated and used to efficiently synthesize two different monomers (16-hydroxy-10-oxo-hexadecanoic and 7-oxohexa-decanedioic acids) in addition to a dimer and linear and branched trimers. These compounds were fully characterized using NMR and MS techniques and could be used as starting materials for the synthesis of a wide range of chemicals and bio-polyesters, particularly the latter due to their physical properties, non-toxicity, and relative abundance among raw materials.

A comparison of suberin monomers from the multiseriate exodermis of Iris germanica during maturation under differing growth conditions

Iris germanica roots develop a multiseriate exodermis (MEX) in which all mature cells contain suberin lamellae. The location and lipophilic nature of the lamellae contribute to their function in restricting radial water and solute transport. The objective of the current work was to identify and quantify aliphatic suberin monomers, both soluble and insoluble, at specific stages of MEX development and under differing growth conditions, to better understand aliphatic suberin biosynthesis. Roots were grown submerged in hydroponic culture, wherein the maturation of up to three exodermal layers occurred over 21 days. In contrast, when roots were exposed to a humid air gap, MEX maturation was accelerated, occurring within 14 days. The soluble suberin fraction included fatty acids, alkanes, fatty alcohols, and ferulic acid, while the suberin poly(aliphatic) domain (SPAD) included fatty acids, α,ω-dioic acids, ω-OH fatty acids, and ferulic acid. In submerged roots, SPAD deposition increased with each layer, although the composition remained relatively constant, while the composition of soluble components shifted toward increasing alkanes in the innermost layers. Air gap exposure resulted in two significant shifts in suberin composition: nearly double the amount of SPAD monomers across all layers, and almost three times the alkane accumulation in the first layer. The localized and abundant deposition of C18:1 α,ω-dioic and ω-OH fatty acids, along with high accumulation of intercalated alkanes in the first mature exodermal layer of air gap-exposed roots indicate its importance for water retention under drought compared with underlying layers and with entire layers developing under water.

Water and solute permeabilities of Arabidopsis roots in relation to the amount and composition of aliphatic suberin

Although it is implied that suberized apoplastic barriers of roots negatively correlate with water and solute permeabilities, direct transport measurements across roots with altered amounts and compositions of aliphatic suberin are scarce. In the present study, hydroponically grown Arabidopsis wild types (Col8 and Col0) and different suberin mutants with altered amounts and/or compositions (horst, esb1-1, and esb1-2) were used to test this hypothesis. Detailed histochemical studies revealed late development of Casparian bands and suberin lamellae in the horst mutant compared with wild types and esb mutants. Suberin analysis with gas chromatography and mass spectrometry (GC-MS) showed that the horst mutant had ∼33% lower amounts of aliphatic monomers than Col8 and Col0. In contrast, enhanced suberin mutants (esb1-1 and esb1-2) had twice the amount of suberin as the wild types. Correlative permeability measurements, which were carried out for the first time with a root pressure probe for Arabidopsis, revealed that the hydraulic conductivity (Lp(r)) and NaCl permeability (P(sr)) of the whole root system of the horst mutant were markedly greater than in the respective wild types. This was reflected by the total amounts of aliphatic suberin determined in the roots. However, increased levels of aliphatic suberin in esb mutants failed to reduce either water or NaCl permeabilities below those of the wild types. It was concluded that the simple view and the conventional assumption that the amount of root suberin negatively correlates with permeability may not always be true. The aliphatic monomer arrangement in the suberin biopolymer and its microstructure also play a role in apoplastic barrier formation.

Suberin research in the genomics era--new interest for an old polymer

Suberin is an apoplastic biopolymer with tissue-specific deposition in the cell walls of the endo- and exodermis of roots, of periderms including wound periderm and other border tissues. Suberised cell walls contain both polyaliphatic and polyaromatic domains which are supposedly cross-linked. The predominant aliphatic components are ω-hydroxyacids, α,ω-diacids, fatty acids and primary alcohols, whereas hydroxycinnamic acids, especially ferulic acid, are the main components of the polyaromatic domain. Although the monomeric composition of suberin has been known for decades, its biosynthesis and deposition has mainly been a subject of speculation. Only recently, significant progress elucidating suberin biosynthesis has been achieved using molecular genetic approaches, especially in the model species Arabidopsis. In parallel, the long-standing hypothesis that suberin functions as an apoplastic barrier has been corroborated by sophisticated, quantitative physiological studies in the past decade. These studies demonstrated that suberised cell walls could act as barriers, minimising the movement of water and nutrients, restricting pathogen invasion and impeding toxic gas diffusion. In addition, suberised cell walls provide a barrier to radial oxygen loss from roots to the anaerobic root substrate in wetland plants. The recent onset of multidisciplinary approaches combining genetic, analytical and physiological studies has begun to deliver further insights into the physiological importance of suberin depositions in plants.

Basis of a humeomics science: chemical fractionation and molecular characterization of humic biosuprastructures

We propose a mild stepwise fractionation of molecular components of a humic acid (HA) suprastructure and their structural identification by advanced analytical methods. This procedure may be the basis of a "Humeomics" approach to characterize natural humic molecules and clarify their relations with ecosystems functions. Sequential fractionation included: (1) organic solvent extraction, (2) transesterification with boron trifluoride in methanol (BF(3)-CH(3)OH), (3) methanolic alkaline hydrolysis (KOH-CH(3)OH), and (4) cleavage of ether and glycosidic bonds with HI. Structural identification of initial and final material, separated organo-soluble and hydrosoluble fractions, and subfractions was conducted by GC-MS, HPSEC-ESI-MS (high-resolution, Orbitrap), and solid- and liquid-state NMR. GC-MS revealed in organosoluble unbound fractions the presence of both saturated and unsaturated, linear and branched, alkanoic, hydroxyalkanoic and alkandioic acids, n-alkanes, and n-alkanols. These components decreased progressively in fractions obtained after weak and strong ester cleavage. Unsubstituted alkanoic acids with variable chain length were ubiquitously detected in all fractions, thereby suggesting their fundamental function in the architecture of humic suprastructures. An important role in differentiating supramolecular associations should also be attributed to substituted alkanoic acids that were detected in variable amounts in different fractions. The content of aromatic acids and steroids was only noticed in the latter fractions. HPSEC-ESI-MS of initial and final solid fractions showed similar compounds, as indicated by GC-MS, whereas the hydrosoluble fraction after transesterification revealed fewer of these compounds but noticeable nitrogen-containing acids. A large amount of "cyclic" acids were identified by MS empirical formula in initial HA, and, to a lesser extent, in the final fractionation residue as well as in the hydrosoluble fraction. The predominant alkyl NMR signals in organosoluble extracts and those of CH-N, CH-O, and O-CH-O groups in hydrosoluble fraction confirmed mass spectrometry results. Homo- and heterocorrelated liquid-state NMR spectra indicated spin systems interactions varying with separated fractions. Solid-state and dipolar-dephasing NMR spectra of final residue showed predominance of sp(2) carbons, 66% of which were quaternary carbons, and a significant increase in conformational rigidity with respect to initial HA. Separated fractions accounted for 60% of initial HA weight, and losses were attributed to hydration water, liberated volatile compounds, and decarboxylation. Quantization of analytes showed that the sum of compound classes in separated fractions was greater than that for the initial HA, thereby showing that stepwise fractionation increased significantly the analytical identification of humic molecules. Our results suggest this "Humeomics" approach as a valid path for mapping humic molecular composition and assess humus origin and formation.

Improved lateral discrimination in screening the elemental composition of buckwheat grain by micro-PIXE

The elemental composition of specific fractions of cereal and pseudocereal grains can be roughly estimated after milling. Alternatively, the elemental localization of cross-sectioned grains can be quantitatively analyzed by microproton induced X-ray emission (micro-PIXE), taking advantage of high elemental sensitivity and low lateral resolution. We present a micro-PIXE study on buckwheat (Fagopyrum esculentum) grain, with a detailed description of the elemental distributions. Elements such as Mg, P, S, K, Fe, Ni, Cu, and Zn were preferentially localized in the cotyledons and embryonic axis; however, significant amounts of K and Fe were also found in the pericarp. The aleurone layer covering the cotyledons was especially enriched in S and P, while testa, a thin layer above the aleurone did not show any significant element enrichments. The highest concentrations of Al, Si, Cl, Ca, and Ti were found in the pericarp. A detailed element localization study of pericarp layers revealed that the inner layer was enriched in K, Mn, Ca, and Fe, while the outer layer showed enrichments in Na, Mg, P, S, and Al. On the basis of the data obtained, milling techniques can be adapted to obtain milling fractions with targeted nutritional values.

Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition

Suberin is a protective hydrophobic barrier consisting of phenolics, glycerol, and a variety of fatty acid derivatives, including C18:0-C22:0 primary fatty alcohols. An eight-member gene family encoding alcohol-forming fatty acyl-coenzyme A reductases (FARs) has been identified in Arabidopsis (Arabidopsis thaliana). Promoter-driven expression of the beta-glucuronidase reporter gene indicated that three of these genes, FAR1(At5g22500), FAR4(At3g44540), and FAR5(At3g44550), are expressed in root endodermal cells. The three genes were transcriptionally induced by wounding and salt stress. These patterns of gene expression coincide with known sites of suberin deposition. We then characterized a set of mutants with T-DNA insertions in FAR1, FAR4, or FAR5 and found that the suberin compositions of roots and seed coats were modified in each far mutant. Specifically, C18:0-OH was reduced in far5-1, C20:0-OH was reduced in far4-1, and C22:0-OH was reduced in far1-1. We also analyzed the composition of polymer-bound lipids of leaves before and after wounding and found that the basal levels of C18:0-C22:0 primary alcohols in wild-type leaves were increased by wounding. In contrast, C18:0-OH and C22:0-OH were not increased by wounding in far5-1 and far1-1 mutants, respectively. Heterologous expression of FAR1, FAR4, and FAR5 in yeast confirmed that they are indeed active alcohol-forming FARs with distinct, but overlapping, chain length specificities ranging from C18:0 to C24:0. Altogether, these results indicate that Arabidopsis FAR1, FAR4, and FAR5 generate the fatty alcohols found in root, seed coat, and wound-induced leaf tissue.

Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region-specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone

In water-stressed soybean primary roots, elongation was maintained at well-watered rates in the apical 4 mm (region 1), but was progressively inhibited in the 4-8 mm region (region 2), which exhibits maximum elongation in well-watered roots. These responses are similar to previous results for the maize primary root. To understand these responses in soybean, spatial profiles of soluble protein composition were analysed. Among the changes, the results indicate that region-specific regulation of phenylpropanoid metabolism may contribute to the distinct growth responses in the different regions. Several enzymes related to isoflavonoid biosynthesis increased in abundance in region 1, correlating with a substantial increase of isoflavonoid content in this region which could contribute to growth maintenance via various potential mechanisms. In contrast, caffeoyl-CoA O-methyltransferase, which is involved in lignin synthesis, was highly up-regulated in region 2. This response was associated with enhanced accumulation of lignin, which may be related to the inhibition of growth in this region. Several proteins that increased in abundance in both regions of water-stressed roots were related to protection from oxidative damage. In particular, an increase in the abundance of ferritin proteins effectively sequestered more iron and prevented excess free iron in the elongation zone under water stress.

A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis

Suberin, a polyester polymer in the cell wall of terrestrial plants, controls the transport of water and nutrients and protects plant from pathogenic infections and environmental stresses. Structurally, suberin consists of aliphatic and aromatic domains; p-hydroxycinnamates, such as ferulate, p-coumarate, and/or sinapate, are the major phenolic constituents of the latter. By analyzing the "wall-bound" phenolics of mutant lines of Arabidopsis deficient in a family of acyl-CoA dependent acyltransferase (BAHD) genes, we discovered that the formation of aromatic suberin in Arabidopsis, primarily in seed and root tissues, depends on a member of the BAHD superfamily of enzymes encoded by At5g41040. This enzyme exhibits an omega-hydroxyacid hydroxycinnamoyltransferase activity with an in vitro kinetic preference for feruloyl-CoA and 16-hydroxypalmitic acid. Knocking down or knocking out the At5g41040 gene in Arabidopsis reduces specifically the quantity of ferulate in suberin, but does not affect the accumulation of p-coumarate or sinapate. The loss of the suberin phenolic differentially affects the aliphatic monomer loads and alters the permeability and sensitivity of seeds and roots to salt stress. This highlights the importance of suberin aromatics in the polymer's function.

On the diversity of the laccase gene: a phylogenetic perspective from Botryosphaeria rhodina (Ascomycota: Fungi) and other related taxa

The present study is the first describing the sequencing of a fragment of the copper-oxidase domain of a laccase gene in the family Botryosphaeriaceae. The aim of this work was to assess the degree of genetic and evolutionary relationships of a laccase gene from Botryosphaeria rhodina MAMB-05 with other ascomycete and basidiomycete laccase genes. The 193-amino acid sequences of the copper-oxidase domain from several different fungi, insects, a plant, and a bacterial species were retrieved from GenBank and aligned. Phylogenetic analyses were performed using neighbor-joining, maximum parsimony, and Bayesian inference methods. The organisms studied clustered into five gene clades: fungi (ascomycetes and basidiomycetes), insects, plants, and bacteria. Also, the topologies showed that fungal laccases of the ascomycetes and basidiomycetes are clearly separated into two distinct clusters. This evidence indicated that B. rhodina MAMB-05 and other closely related ascomycetes are a new biological resource given the biotechnological potential of their laccase genes.

The DAISY gene from Arabidopsis encodes a fatty acid elongase condensing enzyme involved in the biosynthesis of aliphatic suberin in roots and the chalaza-micropyle region of seeds

Suberin is a hydrophobic polyester found in the cell walls of various plant-environment interfaces, including shoot and root peridermal tissue, and the root hypodermis and endodermis. Suberin deposits form apoplastic barriers that control water and nutrient transport, protect against pathogens and seal wounded tissue. Despite this physiological importance, and the detailed information on the suberin composition of many plants, there is a great gap in our knowledge of the molecular mechanism of suberin biosynthesis, caused in part by a lack of mutants in suberin formation. Here, we report the characterization of daisy, an Arabidopsis mutant that is defective in a fatty acid elongase condensing enzyme. The daisy mutant roots exhibit disturbed growth, and the suberin level is reduced in C(22) and C(24) very long chain fatty acid derivatives, whereas C(16), C(18) and C(20) derivatives accumulate, compared with wild-type suberin, indicating that DAISY functions as a docosanoic acid synthase. Consistent with a significantly increased level of suberin in the roots of NaCl-stressed plants, DAISY is transcriptionally activated by NaCl application, and also by polyethylene glycol-induced drought stress and wounding. Expression analysis using RT-PCR and promoter-GUS fusions demonstrated a distinct DAISY expression pattern in the root stele, senescing sepals, siliques abscission zones and the chalaza-micropyle region of seeds. Together, these results indicate that DAISY is involved in suberin biosynthesis and in the formation of protective layers in these tissues, and in the response to unfavourable environmental conditions.

Anatomical and chemical alterations but not photosynthetic dynamics and apoplastic transport changes are involved in the brittleness culm mutation of rice

Brittleness culm is an important agronomic trait that has a potential usefulness in agricultural activity as animal forage although the developmental mechanism is not clear yet. In the present study, the anatomical and chemical characteristics as well as some ecophysiological features in the brittleness culm mutation of rice (Oryza sativa L.) were investigated. Compared with the wild type (WT), the brittleness culm mutant (bcm) exhibited higher culm vascular bundle distance and lower culm wall thickness, leaf interveinal distance and leaf thickness. Ratio of bundle sheath cell/whole bundle and areas of whole vascular bundles and bundle sheath of leaves were reduced while ratios of xylem and phloem to whole bundles were elevated in bcm. The Fourier transform infrared (FTIR) microspectroscopy analysis and further histochemical and physiological measurements revealed that the different contents and depositions of cell wall components such as pectins, lignin, suberin and cellulose all participated in the mutation of brittleness. However, the mutant presented no significant changes in leaf photosynthetic dynamics and apoplastic transport ability. These results strongly indicate that the alterations in anatomical and chemical characteristics, rather than changes in major ecophysiological features such as photosynthesis and apoplastic transport were involved in the brittleness mutation of rice.

Effect of potato suberin on Streptomyces scabies proteome

Two-dimensional (2D) PAGE was used to detect proteins induced in Streptomyces scabies by potato suberin, a lipidic plant polymer. Nineteen up-regulated proteins were excised from 2D gels and analysed by N-terminal sequencing or tandem mass spectrometry (MS/MS). Four of the up-regulated proteins could be linked to the bacterial response to stress (AldH, GroES, TerD and LexA). Specific metabolic pathways seemed to be activated in the presence of suberin, as shown by the increased expression of specific transporters and of enzymes related not only to glycolysis, but also to nucleotide and amino acid metabolism. Suberin also appeared to influence secondary metabolism as it also caused the overproduction of the BldK proteins that are known to be involved in differentiation and secondary metabolism.