Function identification of Arabidopsis GPAT4 and GPAT8 in the biosynthesis of suberin and cuticular wax

Surface lipids in plants include cutin, cuticular wax and suberin. sn-Glycerol-3-phosphate acyltransferases (GPATs) facilitate the acylation of sn-glycerol-3-phosphate (G3P) utilizing a fatty acyl group from acyl-coenzyme A (acyl-CoA) or acyl-acyl carrier protein (acyl-ACP) as substrates for the biosynthesis of plant extracellular lipids such as suberin and cutin. Here we found that Arabidopsis GPAT4 and GPAT8 are specifically expressed in endodermis cells of roots where suberin was accumulated. GPAT4 mutation significantly decreased the amounts of the C16 and C18 ω-oxidized suberin monomers, whereas the mutation of GPAT8 had little effect on the suberin production, and the functions of both were not redundant. Root suberin phenotype analysis of gpat4-1 and gpat6-1 single or double mutant revealed that GPAT4 and GPAT6 play redundant functions. Interestingly, the gpat4-1 gpat8-1 double mutant displayed a glossy stem phenotype since fewer wax crystals were accumulated. This phenotype was not shown in either parent. Further study showed that the amounts of most wax components were significantly decreased. Taken together, our findings revealed that GPAT4 has an additive effect with GPAT6 in the root suberin biosynthesis, and plays a redundant role in wax production with GPAT8.

13C dicarboxylic acid signatures indicate temporal shifts in catchment sediment sources in response to extreme winter rainfall

Rainfall and land-use interactions drive temporal shifts in suspended sediment sources, yet the magnitude of such changes remains poorly understood due to the lack of land-use specific source tracers. We investigated α,ω-dicarboxylic fatty acid root-specific biomarkers, as diagnostic tracers for apportioning sources of time-integrated suspended sediment samples collected from a grassland dominated agricultural catchment in the southwest of England during the wet winter period. Applying fatty acids-specific stable carbon isotope analysis and a Bayesian isotope mixing model, we show that stream banks contributed most of the sediment in the early winter, i.e. October-December, while winter cereal-dominated arable land contributed more than half of the sediment during the late winter, i.e. January-March. The dominant sediment source shifted in conjunction with a period of prolonged consecutive rainfall days in the later period suggesting that intervention required to mitigate soil erosion and sediment delivery should adapt to changing rainfall patterns. Our novel findings demonstrate that isotopic signatures of α,ω-dicarboxylic fatty acids are promising tracers for understanding the resistance of agricultural soils to water erosion and quantifying the interactive effects of extreme rainfall and land use on catchment sediment source dynamics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10311-023-01684-1.

Determination of De Novo Suberin-Lignin Ferulate Deposition in Xylem Tissue Upon Vascular Pathogen Attack

Plant vascular pathogens use different ways to reach the xylem vessels and cause devastating diseases in plants. Resistant and tolerant plants have evolved various defense mechanisms against vascular pathogens. Inducible physico-chemical structures, such as the formation of tyloses and wall reinforcements with phenolic polymers, are very effective barriers that confine the pathogen and prevent colonization. Here, we use a combination of classical histochemistry along with bright-field and fluorescence microscopy and two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy to visualize and characterize wall reinforcements containing phenolic wall polymers, namely, lignin, ferulates, and suberin, which occur in different xylem vasculature in response to pathogen attack.

The exodermis: A forgotten but promising apoplastic barrier

The endodermis and exodermis are widely recognized as two important barriers in plant roots that play a role in regulating the movement of water and ions. While the endodermis is present in nearly all plant roots, the exodermis, characterized by Casparian strips and suberin lamellae is absent in certain plant species. The exodermis can be classified into three types: uniform, dimorphic, and inducible exodermis. Apart from its role in water and ion transport, the exodermis acts as a protective barrier against harmful substances present in the external environment. Furthermore, the exodermis is a complex barrier influenced by various environmental factors, and its resistance to water and ions varies depending on the type of exodermis and the maturity of the root. Therefore, investigations concerning the exodermis necessitate a plant-specific approach. However, our current understanding of the exodermal physiological functions and molecular mechanisms governing its development is limited due to the absence of an exodermis in the model plant Arabidopsis. Due to that, unfortunately, the exodermis has been largely overlooked until now. In this review, we aim to summarize the current fundamental knowledge regarding the exodermis in common research used crop species and propose suggestions for future research endeavors.

Cork cellular and chemical features underlying bark environmental protection in the miombo species Parinari curatellifolia

Parinari curatellifolia is an important evergreen tree from the Miombo woodland of south-central and eastern Africa. The bark is corky, suggesting an increased protection against the ecosystem high temperatures and drought conditions as well as against wild fires. The cork in the bark rhytidome of P. curatellifolia was analyzed here for the first time with a focus on chemical and cellular features. P. curatellifolia cork has the cellular characteristics of cork tissues, with typical honeycomb structure in the tangential section and a brick-wall layer in the transverse and radial sections, without intercellular voids. Chemically P. curatellifolia cork has 8.4 % extractives, 33.9 % suberin, 31.9 % lignin and 25.2 % polysaccharides of the cork. The hemicelluloses are mostly xylans, with a substantial proportion of arabinose and galactose. Suberin showed a proportion of long chain lipids to glycerol (LCLip:Gly, mass ratio) of 8.5, and the long chain monomeric composition included a similar proportion of α,ω-diacids and ω-hydroxy acids (35.4 % and 31.5 % of long chain monomers) with a substantial proportion of monoacids (19.4 % of long chain monomers). Lignin is a guaiacyl-syringyl lignin with S/G of 0.32 and H:G:S of 1:14.1:4.5. The rhytidome composition and the cellular and chemical features of its cork are in line with environment-targeted protective features namely as a transpiration and insulation barrier, and as an increased fire protection.

Time course of changes in the transcriptome during russet induction in apple fruit

BACKGROUND

Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

RESULTS

During moisture exposure (Phase I) of 'Pinova' apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

CONCLUSIONS

The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.

Comprehensive analysis of KCS gene family in pear reveals the involvement of PbrKCSs in cuticular wax and suberin synthesis and pear fruit skin formation

Cuticular wax, cutin and suberin polyesters covering the surface of some fleshy fruit are tightly associated with skin color and appearance. β-Ketoacyl-CoA synthase (KCS) is a rate-limiting enzyme participating in the synthesis of very-long-chain fatty acids (VLCFAs), the essential precursors of cuticular waxes and aliphatic monomers of suberin. However, information on the KCS gene family in pear genome and the specific members involved in pear fruit skin formation remain unclear. In the present study, we performed an investigation of the composition and amount of cuticular waxes, cutin and aliphatic suberin in skins of four sand pear varieties with distinct colors (russet, semi-russet, and green) and demonstrated that the metabolic shifts of cuticular waxes and suberin leading to the significant differences of sand pear skin color. A genome-wide identification of KCS genes from the pear genome was conducted and 35 KCS coding genes were characterized and analyzed. Expression profile analysis revealed that the KCS genes had diverse expression patterns among different pear skins and the transcript abundance of PbrKCS15, PbrKCS19, PbrKCS24, and PbrKCS28 were consistent with the accumulation of cuticular waxes and suberin in fruit skin respectively. Subcellular localization analysis demonstrated that PbrKCS15, PbrKCS19, PbrKCS24 and PbrKCS28 located on the endoplasmic reticulum (ER). Further, transient over-expression of PbrKCS15, PbrKCS19, and PbrKCS24 in pear fruit skins significantly increased cuticular wax accumulation, whereas PbrKCS28 notably induced suberin deposition. In conclusion, pear fruit skin color and appearance are controlled in a coordinated way by the deposition of the cuticular waxes and suberin. PbrKCS15, PbrKCS19, and PbrKCS24 are involved in cuticular wax biosynthesis, and PbrKCS28 is involved in suberin biosynthesis, which play essential roles in pear fruit skin formation. Moreover, this work provides a foundation for further understanding the functions of KCS genes in pear.

Nitrate_dependent suberization regulates cadmium uptake and accumulation in maize

In this study, effect of nitrate-dependent suberization in maize root on cadmium (Cd) uptake and accumulation was investigated. Suberization in maize roots was significantly lower in plants grown with a high nitrate supply compared with low nitrate. This decrease was seen in the total amount of suberin, in which the aliphatic suberin amount was significantly decreased, whereas no difference in aromatic suberin content between different N-treatments. RNA-sequencing showed that suberin biosynthesis genes were upregulated in low nitrate treatment, which correlated well with the increased suberin content. Bioimaging and xylem sap analysis showed that reduced exodermal and endodermal suberization in roots of plants grown under high nitrate promoted radial Cd transport along the crown root. The enhanced suberization in crown roots of plants grown in low nitrate restricted the radial transport of Cd from epidermis to cortex via decreased accessibility to Cd related transporters at the plasmalemma. Also, under low nitrate supply, the Cd transport gene ZmNramp5 was upregulated in the crown root, which may enhance Cd uptake by root tip where exodermis and endodermis were not fully suberized. These results suggest that high nitrate supply enhances Cd uptake and radial transport in maize roots by reducing exodermal and endodermal suberization.

Selenite reduced uptake/translocation of cadmium via regulation of assembles and interactions of pectins, hemicelluloses, lignins, callose and Casparian strips in rice roots

Selenium (Se) can reduce cadmium (Cd) uptake/translocation via regulating pectins, hemicelluloses and lignins of plant root cell walls, but the detailed molecular mechanisms are not clear. In this study, six hydroponic experiments were set up to explore the relationships of uptake/translocation inhibition of Cd by selenite (Se(IV)) with cell wall component (CWC) synthesis and/or interactions. Cd and Se was supplied (alone or combinedly) at 1.0 mg L^-1 and 0.5 mg L^-1, respectively, with the treatment without Cd and Se as the control. When compared to the Cd1 treatment, the Se0.5Cd1 treatment 1) significantly increased total sugar concentrations in pectins, hemicelluloses and callose, suggesting an enhanced capacity of binding Cd or blocking Cd translocation; 2) stimulated the deposition of Casparian strips (CS) in root endodermis and exodermis to block Cd translocation; 3) stimulated the release of C-O-C (-OH^- or -O^-) and CO (carboxyl, carbonyl, or amide) to combine Cd; 4) regulated differential expression genes (DEGs) and metabolites (DMs) correlated with synthesis and/or interactions of CWSs to affect cell wall net structure to affect root cell division, subsequent root morphology and finally elemental uptake; and 5) stimulated de-methylesterification of pectins via reducing expression abundances of many DMs and DEGs in the Yang Cycle to reduce supply of methyls to homogalacturonan, and regulated gene expressions of pectin methylesterase to release carboxyls to combine Cd; and 6) down-regulated gene expressions associated with Cd uptake/translocation.

The Arabidopsis thaliana Gulono-1,4 γ-lactone oxidase 2 (GULLO2) facilitates iron transport from endosperm into developing embryos and affects seed coat suberization

Plants synthesize ascorbate (ASC) via the D-mannose/L-galactose pathway whereas animals produce ASC and H₂O₂via the UDP-glucose pathway, with Gulono-1,4 γ-lactone oxidases (GULLO) as the last step. A. thaliana has seven isoforms, GULLO1-7; previous in silico analysis suggested that GULLO2, mostly expressed in developing seeds, might be involved in iron (Fe) nutrition. We isolated atgullo2-1 and atgullo2-2 mutants, quantified ASC and H₂O₂ in developing siliques, Fe(III) reduction in immature embryos and seed coats. Surfaces of mature seed coats were analysed via atomic force and electron microscopies; suberin monomer and elemental compositions of mature seeds, including Fe, were profiled via chromatography and inductively coupled plasma-mass spectrometry. Lower levels of ASC and H₂O₂ in atgullo2 immature siliques are accompanied by an impaired Fe(III) reduction in seed coats and lower Fe content in embryos and seeds; atgullo2 seeds displayed reduced permeability and higher levels of C18:2 and C18:3 ω-hydroxyacids, the two predominant suberin monomers in A. thaliana seeds. We propose that GULLO2 contributes to ASC synthesis, for Fe(III) reduction into Fe(II). This step is critical for Fe transport from endosperm into developing embryos. We also show that alterations in GULLO2 activity affect suberin biosynthesis and accumulation in the seed coat.

PpyMYB144 transcriptionally regulates pear fruit skin russeting by activating the cytochrome P450 gene PpyCYP86B1

PpyMYB144 directly activates the promoter of PpyCYP86B1, promotes the synthesis of α, ω-diacids, and involves in pear fruit skin russeting. Russeting is an economically important surface disorder in pear (Pyrus pyrifolia) fruit. Previous research has demonstrated that suberin is the pivotal chemical component contributing to pear fruit skin russeting, and fruit bagging treatment effectively reduces the amount of suberin of fruits, and thereby reduces the russeting phenotype. However, the mechanisms of pear fruit skin russeting remain largely unclear, particularly the transcriptional regulation. Here, we dissected suberin concentration and composition of pear fruits along fruit development and confirmed that α, ω-diacids are the predominant constituents in russeted pear fruit skins. Two cytochrome P450 monooxygenase (CYP) family genes (PpyCYP86A1 and PpyCYP86B1) and nine MYB genes were isolated from pear fruit. Expressions of PpyCYP86A1, PpyCYP86B1, and five MYB genes (PpyMYB34, PpyMYB138, PpyMYB138-like, PpyMYB139, and PpyMYB144) were up-regulated during fruit russeting and showed significant correlations with the changes of α, ω-diacids. In addition, dual-luciferase assays indicated that PpyMYB144 could trans-activate the promoter of PpyCYP86B1, and the activation was abolished by motif mutagenesis of AC element on the PpyCYP86B1 promoter. Further, Agrobacterium-mediated transient expression of PpyCYP86B1 and PpyMYB144 in pear fruits induced the deposition of aliphatic suberin. Thus, PpyMYB144 is a novel direct activator of PpyCYP86B1 and contributes to pear fruit skin russeting.

Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Suberin deposition involves both phenolic and aliphatic polymer biosynthesis and deposition in the same tissue. Therefore, any consideration of exploiting suberin for crop enhancement (e.g., enhanced storage, soil borne disease resistance) requires knowledge of both phenolic and aliphatic component biosynthesis and their coordinated, temporal deposition. In the present study, we use a wound-healing potato tuber system to explore global transcriptome changes during the early stages of wound-healing. Wounding leads to initial and substantial transcriptional changes that follow distinctive temporal patterns - primary metabolic pathways were already functional, or up-regulated immediately, and maintained at levels that would allow for precursor carbon skeletons and energy to feed into downstream metabolic processes. Genes involved in pathways for phenolic production (i.e., the shikimate pathway and phenylpropanoid metabolism) were up-regulated early while those involved in aliphatic suberin production (i.e., fatty acid biosynthesis and modification) were transcribed later into the time course. The pattern of accumulation of genes associated with ABA biosynthesis and degradation steps support a role for ABA in regulating aliphatic suberin production. Evaluation of putative Casparian strip membrane-like genes pinpointed wound-responsive candidates that may mediate the suberin deposition process.

Organic matter biomarker and 13C NMR characteristics of soil and sediment standard reference materials from China

Soil and sediment organic matter (OM) in terrestrial environments represent two critical organic carbon pools on Earth and are likely subject to distinct degrees of oxidation and modification. However, few studies have identified critical molecular-level characteristics that differentiate soil and sediment OM from various climate zones. Using biomarkers and solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy analyses, we studied the OM characteristics of 11 soil and 7 sediment standard reference materials (SRMs) originating from various geographical locations in China. Results showed significantly higher concentrations of lignin phenols in sediment OM than in soil OM, which may result from protection by higher contents of CaO and less microbial degradation in sediments. Nevertheless, the relative abundances of solvent-extractable lipids (alkanes, alkanols, and alkanoic acids) and ester-bound cutin and suberin biomarkers did not differ significantly between soil and sediment SRMs. The concentrations of lignin biomarkers decreased with increasing weathering degree of the soil, while cutin biomarkers increased with mean annual temperature and precipitation. This phenomenon was not observed in sediment SRMs. This study reveals the distinct OM characteristics between Chinese soil and sediment SRMs and provides fundamental data for future studies to link OM characteristics and functions.

Building and breaking of a barrier: Suberin plasticity and function in the endodermis

Plant cells coated with hydrophobic compounds constitute a protective barrier to control movement of materials through plant tissues. In roots, the endodermis develops two barriers: the Casparian strips establish an apoplastic barrier and suberin lamellae prevent diffusion through the plasma membrane. Suberin is a complex biopolymer and its deposition is highly responsive to the environment. While the enzymatic framework involved in suberin biosynthesis is well characterized, subsequent steps in suberin formation and regulation remained elusive. Recent publications, studying suberin from a cell biological perspective, have enriched our knowledge on suberin transport and polymerization in the cell wall. These studies have also elucidated the molecular mechanisms controlling suberin biosynthesis and regulation as well as its physiological role in plant abiotic and biotic interactions.

Visualizing polymeric components that define distinct root barriers across plant lineages

Hydrophobic cell wall depositions in roots play a key role in plant development and interaction with the soil environment, as they generate barriers that regulate bidirectional nutrient flux. Techniques to label the respective polymers are emerging, but are efficient only in thin roots or sections. Moreover, simultaneous imaging of the barrier constituents lignin and suberin remains problematic owing to their similar chemical compositions. Here, we describe a staining method compatible with single- and multiphoton confocal microscopy that allows for concurrent visualization of primary cell walls and distinct secondary depositions in one workflow. This protocol permits efficient separation of suberin- and lignin-specific signals with high resolution, enabling precise dissection of barrier constituents. Our approach is compatible with imaging of fluorescent proteins, and can thus complement genetic markers or aid the dissection of barriers in biotic root interactions. We further demonstrate applicability in deep root tissues of plant models and crops across phylogenetic lineages. Our optimized toolset will significantly advance our understanding of root barrier dynamics and function, and of their role in plant interactions with the rhizospheric environment.

Precursor biosynthesis regulation of lignin, suberin and cutin

The extracellular matrix of plants can contain the hydrophobic biopolymers lignin, suberin and/or cutin, which provide mechanical strength and limit water loss and pathogen invasion. Due to their remarkable chemical resistance, these polymers have a high potential in various biotechnological applications and can replace petrol-based resources, for example, in the packing industry. However, despite the importance of these polymers, the regulation of their precursor biosynthesis is far from being fully understood. This is particularly true for suberin and cutin, which hinders efforts to engineer their formation in plants and produce customised biopolymers. This review brings attention to knowledge gaps in the current research and highlights some of the most recent findings on transcription factors that regulate lignin, suberin and cutin precursor biosynthesis. Finally, we also briefly discuss how some of the remaining knowledge gaps can be closed.

Silicon alleviates antimony phytotoxicity in giant reed (Arundo donax L.)

Silicon enhances photosynthetic efficiency, biomass, and lignification of root structures possibly limiting antimony translocation and mitigating phytotoxicity in giant reed plants. Antimony (Sb) is a non-essential metalloid causing toxic effects in plants. Silicon has been reported to impart tolerance against biotic and abiotic stress in plants. Fast-growing plant, giant reed (Arundo donax L.) is a promising energy crop, can be a suitable plant for phytoremediation. However, information regarding the tolerance capacity with respect to Sb toxicity and potential of Si to mitigate the Sb phytotoxicity in giant reed are very scarce. Rhizomes of giant reed were grown for ten weeks in hydroponics exposed to Sb, Si, and their combination wherein treatment without Sb/Si served as control. Effect of these treatments on rate of net photosynthesis and photosynthetic pigments, phytoextraction ability of Sb, Si and Sb uptake, plant biomass, and lignification and suberization of roots along with localization of Sb and Si were analysed. We found that Si considerably improved the growth and biomass of giant reed under Sb toxicity. Antimony reduced the photosynthesis and decreased the content of photosynthetic pigments, which was completely alleviated by Si. Silicon amendment to Sb treated plants enhanced root lignification. Silicon enhanced lignification of root structures probably restricted the Sb translocation. However, co-localization of Sb with Si has not been observed neither at the shoot nor at the root levels. Similarly, Sb was also not detected in leaf phytoliths. These findings suggest that Si treatment promotes overall plant growth by improving photosynthetic parameters and decreasing Sb translocation from root to shoot in giant reed by improving root lignification.

Multiple effects of silicon on alleviation of nickel toxicity in young maize roots

Although beneficial metalloid silicon (Si) has been shown to alleviate the toxicity of various heavy metals, there is a lack of knowledge about the role of Si in possible alleviation of phytotoxicity caused by excess of essential nickel (Ni). In the present study we investigated the growth and biomass production, reactive oxygen species (ROS) formation and activities of selected antioxidants, as well as combined effect of Ni and Si on the integrity of cell membranes and electrolyte leakage in young maize roots treated for 24, 48 and 72 h with excess of Ni and/or Si. By histochemical methods we also visualized Ni distribution in root tissues and compared the uptake of Ni and Si with the development of root apoplasmic barriers. Ni enhanced the root lignification and suberization and shifted the development of apoplasmic barriers towards the root tip. Similarly, localization of Ni correlated with lignin and suberin deposition in root endodermis, further supporting the barrier role of this tissue in Ni uptake. Si reversed the negative impact of Ni on root anatomy. Additionally, improved cell membrane integrity, and enhanced ascorbate-based antioxidant system might be the mechanisms how Si partially mitigates the deleterious effects of Ni excess in maize plants.

Analysis of Extracellular Cell Wall Lipids: Wax, Cutin, and Suberin in Leaves, Roots, Fruits, and Seeds

Extracellular lipids of plants can be analyzed using gas chromatography and mass spectrometry. Soluble waxes are extracted with chloroform and thus separated from the extracellular polymers cutin and suberin. Cutin and suberin have to be depolymerized using boron trifluoride-methanol or methanolic HCl before analysis. The released monomeric hydroxylated fatty acids are then extracted with chloroform or hexane. Prior to gas chromatography, all free polar functional groups (alcohols and carboxylic acids) are derivatized by trimethylsilylation. Internal standards, that is, long chain alkanes, are used for the quantification of wax molecules and cutin or suberin monomers. Lipids are quantified using gas chromatography coupled to flame ionization detection. Qualitative analysis is carried out by gas chromatography coupled to mass spectrometry. Thus, all wax molecules of chain lengths from C₁₆ to C₆₀ and different substance classes (fatty acids, alcohols, esters, aldehydes, alkanes, etc.) or all cutin or suberin monomers of chain lengths from C₁₆ to C₃₂ and different substance classes (hydroxylated fatty acids, diacids, etc.) can be analyzed from one sample.

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome

The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere.

Extracellular lipids of Camelina sativa: Characterization of cutin and suberin reveals typical polyester monomers and unusual dicarboxylic fatty acids

Camelina sativa is relatively drought tolerant and requires less fertilizer than other oilseed crops. Various lipid- and phenolic-based extracellular barriers of plants help to protect them against biotic and abiotic stresses. These barriers, which consist of solvent-insoluble polymeric frameworks and solvent-extractable waxes, include the cuticle of aerial plant surfaces and suberized cell walls found, for example, in periderms and seed coats. Cutin, the polymeric matrix of the cuticle, and the aliphatic domain of suberin are fatty acid- and glycerol-based polyesters. These polyesters were investigated by base-catalyzed transesterification of C. sativa aerial and underground delipidated tissues followed by gas chromatographic analysis of the released monomer mixtures. Seed coat and root suberin had similar compositions, with 18-hydroxyoctadecenoic and 1,18-octadecenedioic fatty acids being the dominant species. Root suberin presented a typical lamellar ultrastructure, but seed coats showed almost imperceptible, faint dark bands. Leaf and stem lipid polyesters were composed of fatty acids (FA), 1,ω-dicarboxylic fatty acids (DCA), ω-hydroxy fatty acids (HFA) and hydroxycinnamic acids (HCA). Dihydroxypalmitic acid (DHP) and caffeic acid were the major constituents of leaf cutin, whereas stem cutin presented similar molar proportions in several monomers across the four classes. Unlike the leaf cuticle, the C. sativa stem cuticle presented lamellar structure by transmission electron microscopy. Flower cutin was dominated by DHP, did not contain aromatics, and presented substantial amounts (>30%) of hydroxylated 1,ω-dicarboxylic acids. We found striking differences between the lipid polyester monomer compositions of aerial tissues of C. sativa and that of its close relatives Arabidopsis thaliana and Brassica napus.

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.

Histochemical Staining of Suberin in Plant Roots

Histological stains are useful tools for characterizing cell shape, arrangement and the material they are made from. Stains can be used individually or simultaneously to mark different cell structures or polymers within the same cells, and to visualize them in different colors. Histological stains can be combined with genetically-encoded fluorescent proteins, which are useful for understanding of plant development. To visualize suberin lamellae by fluorescent microscopy, we improved a histological staining procedure with the dyes Fluorol Yellow 088 and aniline blue. In the complex plant organs such as roots, suberin lamellae are deposited deep within the root on the endodermal cell wall. Our procedure yields reliable and detailed images that can be used to determine the suberin pattern in root cells. The main advantage of this protocol is its efficiency, the detailed visualization of suberin localization it generates in the root, and the possibility of returning to the confocal images to analyze and re-evaluate data if necessary.

Nitrogen depletion enhances endodermal suberization without restricting transporter-mediated root NO3- influx

Roots vary their permeability to aid radial transport of solutes towards xylem vessels in response to nutritional cues. Nitrogen (N) depletion was previously shown to induce early suberization of endodermal cell walls and reduce hydraulic conductivity of barley roots suggesting reduced apoplastic transport of ions (Armand et al., 2019). Suberization may also limit transcellular ion movement by blocking access to transporters (Barberon et al., 2016). The aim of this study was to confirm that N depletion induced suberization in the roots of barley and demonstrate that this was a specific effect in response to NO₃^- depletion. Furthermore, in roots with early and enhanced suberization, we assessed their ability for transporter-mediated NO₃^- influx. N depletion induced lateral root elongation and early and enhanced endodermal suberization of the seminal root of each genotype. Both root to shoot NO₃^- translocation and net N uptake was half that of plants supplied with steady-state NO₃^-. Genes with predicted functions in suberin synthesis (HvHORST) and NO₃^- transport (HvNRT2.2) were induced under N-deplete conditions. N-deplete roots had a higher capacity for high-affinity NO₃^- influx in early suberized roots than under optimal NO₃^-. In conclusion, NO₃^- depletion induced early and enhanced suberization in the roots of barley, however, suberization did not restrict transcellular NO₃^- transport.

Chemical composition of leaf cutin in six Quercus suber provenances

The cutin content and composition of cork oak (Quercus suber) leaves was determined in six provenances with different seed geographical origin spreading across the species natural distribution. The cutin layer on the leaf surface was on average 518 μg/cm² of leaf area and represented 6.7% of the leaf dry weight, with no significant differences among provenances. Cutin depolymerisation was carried out by transesterification on whole leaves. The cutin composition of cork oak leaves is presented here for the first time. It is essentially composed of long-chain aliphatic ω-hydroxy fatty acids (44.4% of the total monomers), mostly with mid-chain hydroxyl and epoxy groups, fatty acids (20.7%), and a smaller proportion of α,ω-dicarboxylic acids (6.5%). The predominant compounds are 10,16-dihydroxy hexadecanoic acid (17.7-25.2%) and 9,10,18-trihydroxyoctadecanoic acid (15.6-18.0%). Alkanols represent 2.8% and aromatic compounds 12.8%, mainly coumarates. Isolation of cuticles from Q. suber leaves was performed using an enzymatic separation procedure and the fragments were analysed. Cuticle isolation is difficult and direct depolymerisation applied to whole leaves proved a suitable method to study cutin monomeric composition, which did not differ substantially to that of the isolated cuticles. No differences between provenances were found regarding cutin content and composition, thereby ruling out a significant genetic determination of these traits, but rather a highly adaptive phenotypic plasticity of cork oak. Although overall similar in their chemical nature, cutin and suberin in cork oak differ in the proportion of the major chemical families, i.e. ω-hydroxy acids, α,ω-diacids, and fatty acids.

The sugarcane ShMYB78 transcription factor activates suberin biosynthesis in Nicotiana benthamiana

KEY MESSAGE

A sugarcane MYB present in the culm induces suberin biosynthesis and is involved both with fatty acid and phenolics metabolism. Few transcription factors have been described as regulators of cell wall polymers deposition in C4 grasses. Particularly, regulation of suberin biosynthesis in this group of plants remains poorly understood. Here, we showed that the sugarcane MYB transcription factor ShMYB78 is an activator of suberin biosynthesis and deposition. ShMYB78 was identified upon screening genes whose expression was upregulated in sugarcane internodes undergoing suberization during culm development or triggered by wounding. Agrobacterium-mediated transient expression of ShMYB78 in Nicotiana benthamiana leaves induced the ectopic deposition of suberin and its aliphatic and aromatic monomers. Further, the expression of suberin-related genes was induced by ShMYB78 heterologous expression in Nicotiana benthamiana leaves. ShMYB78 was shown to be a nuclear protein based on its presence in sugarcane internode nuclear protein extracts, and protoplast transactivation assays demonstrated that ShMYB78 activates the promoters of the sugarcane suberin biosynthetic genes β-ketoacyl-CoA synthase (ShKCS20) and caffeic acid-O-methyltransferase (ShCOMT). Our results suggest that ShMYB78 may be involved in the transcriptional regulation of suberin deposition, from fatty acid metabolism to phenylpropanoid biosynthesis, in sugarcane internodes.

Inhibitors of tri- and tetra- polyamine oxidation, but not diamine oxidation, impair the initial stages of wound-induced suberization

The mechanisms regulating, and modulating potato wound-healing processes are of great importance in reducing tuber infections, reducing shrinkage and maintaining quality and nutritional value for growers and consumers. Wound-induced changes in tuber polyamine metabolism have been linked to the modulation of wound healing (WH) and in possibly providing the crucial amount of H2O2 required for suberization processes. In this investigation we determined the effect of inhibition of specific steps within the pathway of polyamine metabolism on polyamine content and the initial accumulation of suberin polyphenolics (SPP) during WH. The accumulation of SPP represents a critical part of the beginning or inchoate phase of tuber WH during closing-layer formation because it serves as a barrier to bacterial infection and is a requisite for the accumulation of suberin polyaliphatics which provide the barrier to fungal infection. Results showed that the inhibitor treatments that caused changes in polyamine content generally did not influence wound-induced accumulation of SPP. Such lack of correlation was found for inhibitors involved in metabolism and oxidation of putrescine (arginine decarboxylase, ornithine decarboxylase, and diamine oxidase). However, accumulation of SPP was dramatically reduced by treatment with guazatine, a potent inhibitor of polyamine oxidase (PAO), and methylglyoxal-bis(guanylhydrazone), a putative inhibitor of S-adenosylmethione decarboxylase which may also cross-react to inhibit PAO. The mode of action of these inhibitors is presumed to be blockage of essential H2O2 production within the WH cell wall. These results are of great importance in understanding the mechanisms modulating WH and ultimately controlling related infections and associated postharvest losses.

Silencing against the conserved NAC domain of the potato StNAC103 reveals new NAC candidates to repress the suberin associated waxes in phellem

Both suberin and its associated waxes contribute to the formation of apoplastic barriers that protect plants from the environment. Some transcription factors have emerged as regulators of the suberization process. The potato StNAC103 gene was reported as a repressor of suberin polyester and suberin-associated waxes deposition because its RNAi-mediated downregulation (StNAC103-RNAi) over-accumulated suberin and associated waxes in the tuber phellem concomitantly with the induction of representative biosynthetic genes. Here, to explore if other genes of the large NAC gene family participate to this repressive function, we extended the silencing to other NAC members by targeting the conserved NAC domain of StNAC103 (StNAC103-RNAi-c). Transcript profile of the StNAC103-RNAi-c phellem indicated that StNAC101 gene was an additional potential target. In comparison with StNAC103-RNAi, the silencing with StNAC103-RNAi-c construct resulted in a similar effect in suberin but yielded an increased load of associated waxes in tuber phellem, mainly alkanes and feruloyl esters. Globally, the chemical effects in both silenced lines are supported by the transcript accumulation profile of genes involved in the biosynthesis, transport and regulation of apoplastic lipids. In contrast, the genes of polyamine biosynthesis were downregulated. Altogether these results point out to StNAC101 as a candidate to repress the suberin-associated waxes.

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.

Chemical characterization of cork, phloem and wood from different Quercus suber provenances and trees

Sustainability of cork oak (Quercus suber) forests is threatened by biotic and abiotic factors and characterization of potentially differing genetic resources has therefore gained importance. This work addresses the chemical variation of the three tissues of cork oak stems – cork, phloem and wood – in relation to tree and provenance, looking for genetic chemical diversity and for physiological derived differences. The three tissues differ with cork clearly differentiating regarding summative composition, component ratios and monomeric composition. Cork is the only tissue where suberin is present (42.3% o.d. mass) as the main cell wall component, and it has a high content of extractives (11.7%) with significant proportion of lipophilic compounds. Phloem is more lignified than wood (38.0% vs. 23.4%) and has less polysaccharides (49.1% vs. 64.6%) with glucose-to-other sugars relation of 1:1.3 in phloem and 1:0.7 in wood. Analytical pyrolysis showed that lignification is a heterogeneous process and the lignin monomeric composition depends on tissue and cell type: cork lignin has a H:G:S ratio of 1:2.5:0.3 and S/G ratio of 0.12, while phloem and wood lignins have mainly G and S units with a S/G ratio of respectively 1.1 and 2.3. No significant differences were found between the three provenances, but some chemical variation occurred between the trees within a provenance. NIR spectroscopy and principal component analysis differentiated cork, phloem and wood, while the dispersion within each group highlighted the significant tree variability, while provenances were a non-significant factor of chemical variation.

Transcriptome profiling of resistance response to Meloidogyne chitwoodi introgressed from wild species Solanum bulbocastanum into cultivated potato

BACKGROUND

Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it infects potato tubers causing internal as well as external defects, thereby reducing the market value of the crop. Commercial potato varieties with CRKN resistance are currently unavailable. Race specific resistance to CRKN has been introgressed from the wild, diploid potato species Solanum bulbocastanum into the tetraploid advanced selection PA99N82-4 but there is limited knowledge about the nature of its resistance mechanism. In the present study, we performed histological and differential gene expression profiling to understand the mode of action of introgressed CRKN resistance in PA99N82-4 in comparison to the CRKN susceptible variety Russet Burbank.

RESULTS

Histological studies revealed that the nematode juveniles successfully infect both resistant and susceptible root tissue by 48 h post inoculation, but the host resistance response restricts nematode feeding site formation in PA99N82-4. Differential gene expression analysis shows that 1268, 1261, 1102 and 2753 genes were up-regulated in PA99N82-4 at 48 h, 7 days, 14 days and 21 days post inoculation respectively, of which 61 genes were common across all the time points. These genes mapped to plant-pathogen interaction, plant hormonal signaling, antioxidant activity and cell wall re-enforcement pathways annotated for potato.

CONCLUSION

The introgressed nematode resistance in PA99N82-4 is in the form of both pattern-triggered immune response and effector-triggered immune response, which is mediated by accumulation of reactive oxygen species and hypersensitive response (HR). Salicylic acid is playing a major role in the HR. Polyamines and suberin (a component of the Casperian strip in roots) also play an important role in mediating the resistance response. The present study provides the first ever comprehensive insights into transcriptional changes among M. chitwoodi resistant and susceptible potato genotypes after nematode inoculation. The knowledge generated in the present study has implications in breeding for CRKN resistance in potato.

Bacterial release is accompanied by ectopic accumulation of cell wall material around the vacuole in nodules of Pisum sativum sym33-3 allele encoding transcription factor PsCYCLOPS/PsIPD3

Pisum sativum symbiotic mutant SGEFix--2 carries the sym33-3 allele of the gene Sym33, encoding transcription factor PsCYCLOPS/PsIPD3. Previously, strong host cell defence reactions were identified in nodules of this mutant. In the present study, new manifestations of defence reactions were revealed in 28-day-old white nodules in which bacterial release had occurred. These nodules were investigated using histochemical staining of pectin and suberin and by immunogold localisation of three components of pectin: highly methyl-esterified homogalacturonan (HG) recognised by monoclonal antibody JIM7, low methyl-esterified HG recognised by JIM5 and linear (1-4)-β-D-galactan side-chain of rhamnogalacturonan I (RG I) recognised by LM5. In the mutant, but not in the wild-type, cell wall material was deposited around the vacuole in the uninfected cells, in cells containing infection threads and in the infected cells. The deposits around the vacuole were marked with JIM7 and LM5 antibodies but not with JIM5, suggesting that they contain newly formed cell wall material. Deposition was accompanied by suberin accumulation. This is the first report that deposition of cell wall material around the vacuole may be associated with the defence reaction in ineffective nodules. In addition, hypertrophic infection droplets labelled with JIM7 were identified. In the matrix of some infection threads, RG I recognised a pectic gel component. Callose deposits in the cell walls and in the walls of infection threads were occasionally observed. The observations suggest that an important function of transcriptional factor CYCLOPS/IPD3 is the suppression of defence reactions during establishment of the legume-rhizobial symbiosis.

Selected Simple Methods of Plant Cell Wall Histochemistry and Staining for Light Microscopy

Histochemical methods allow for identification and localization of various components within the tissue. Such information on the spatial heterogeneity is not available with biochemical methods. However, there is limitation of the specificity of such detection in context of complex tissue, which is important to consider, and interpretations of the results should regard suitable control treatments if possible. Such methods are valuable extension to specific optical and spectroscopic analytical methods. Here we present a set of selected simple methods of staining and histochemical tests with comments based on our laboratory experience.

Suberized transport barriers in Arabidopsis, barley and rice roots: From the model plant to crop species

Water is the most important prerequisite for life and plays a major role during uptake and transport of nutrients. Roots are the plant organs that take up the major part of water, from the surrounding soil. Water uptake is related to the root system architecture, root growth, age and species dependent complex developmental changes in the anatomical structures. The latter is mainly attributed to the deposition of suberized barriers in certain layers of cell walls, such as endo- and exodermis. With respect to water permeability, changes in the suberization of roots are most relevant. Water transport or hydraulic conductivity of roots (Lp_r) can be described by the composite transport model and is known to be very variable between plant species and growth conditions and root developmental states. In this review, we summarize how anatomical structures and apoplastic barriers of roots can diversely affect water transport, comparing the model plant Arabidopsis with crop plants, such as barley and rice. Results comparing the suberin amounts and water transport properties indicate that the common assumption that suberin amount negatively correlates with water and solute transport through roots may not always be true. The composition, microstructure and localization of suberin may also have a great impact on the formation of efficient barriers to water and solutes.

Plant sn-Glycerol-3-Phosphate Acyltransferases: Biocatalysts Involved in the Biosynthesis of Intracellular and Extracellular Lipids

Acyl-lipids such as intracellular phospholipids, galactolipids, sphingolipids, and surface lipids play a crucial role in plant cells by serving as major components of cellular membranes, seed storage oils, and extracellular lipids such as cutin and suberin. Plant lipids are also widely used to make food, renewable biomaterials, and fuels. As such, enormous efforts have been made to uncover the specific roles of different genes and enzymes involved in lipid biosynthetic pathways over the last few decades. sn-Glycerol-3-phosphate acyltransferases (GPAT) are a group of important enzymes catalyzing the acylation of sn-glycerol-3-phosphate at the sn-1 or sn-2 position to produce lysophosphatidic acids. This reaction constitutes the first step of storage-lipid assembly and is also important in polar- and extracellular-lipid biosynthesis. Ten GPAT have been identified in Arabidopsis, and many homologs have also been reported in other plant species. These enzymes differentially localize to plastids, mitochondria, and the endoplasmic reticulum, where they have different biological functions, resulting in distinct metabolic fate(s) for lysophosphatidic acid. Although studies in recent years have led to new discoveries about plant GPAT, many gaps still exist in our understanding of this group of enzymes. In this article, we highlight current biochemical and molecular knowledge regarding plant GPAT, and also discuss deficiencies in our understanding of their functions in the context of plant acyl-lipid biosynthesis.

A comparative transcriptomic approach to understanding the formation of cork

The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.

In vivo cytological and chemical analysis of Casparian strips using stimulated Raman scattering microscopy

The Casparian strip, a barrier to the apoplastic movement of solutes from the cortex to the stele, is essential for the exclusion of salts, selective nutrient uptake, and many other processes. To date, extensive studies have focused on the physiological functions of endodermal Casparian strips. However, the chemical deposition nature of Casparian strips, as well as its relevance with respect to diffusion barrier functions, remains to be further elucidated. Here, we revealed three developmental stages of Casparian strips in maize primary roots using a traditional fluorescent staining method. Apoplastic permeability tests demonstrated that the barrier function of Casparian strips is largely related to their developmental stage and the pattern of lignin and suberin deposits. Fourier transform infrared (FTIR) analysis showed that the Casparian strips from the roots exhibited significant absorption bands characteristic of lignin and suberin, implying that the Casparian strips in maize primary roots consist largely of lignin and suberin. Furthermore, we developed a new method for label-free, in vivo structural, and biochemical analysis of Casparian strips based on stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we found that lignin and suberin accumulate simultaneously during the Casparian strip formation process. Based on these results, we propose a potential application of SRS for the chemical composition analysis of plant Casparian strips in situ.

Long-term litter manipulation alters soil organic matter turnover in a temperate deciduous forest

Understanding soil organic matter (OM) biogeochemistry at the molecular-level is essential for assessing potential impacts from management practices and climate change on shifts in soil carbon storage. Biomarker analyses and nuclear magnetic resonance (NMR) spectroscopy were used in an ongoing detrital input and removal treatment experiment in a temperate deciduous forest in Pennsylvania, USA, to examine how above- and below-ground plant inputs control soil OM quantity and quality at the molecular-level. From plant material to surface soils, the free acyclic lipids and cutin, suberin, and lignin biomarkers were preferentially retained over free sugars and free cyclic lipids. After 20years of above-ground litter addition (Double Litter) or exclusion (No Litter) treatments, soil OM composition was relatively more degraded, as revealed by solid-state ¹³C NMR spectroscopy. Under Doubled Litter inputs, soil carbon and phospholipid fatty acid (PLFA) concentrations were unchanged, suggesting that the current OM degradation status is a reflection of microbial-mediated degradation that occurred prior to the 20-year sampling campaign. Soil OM degradation was higher in the No Litter treatments, likely due to the decline in fresh, above-ground litter inputs over time. Furthermore, root and root and litter exclusion treatments (No Roots and No Inputs, respectively) both significantly reduced free sugars and PLFAs and increased preservation of suberin-derived compounds. PLFA stress ratios and the low N-acetyl resonances from diffusion edited ¹H NMR also indicate substrate limitations and reduced microbial biomass with these treatments. Overall, we highlight that storage of soil carbon and its biochemical composition do not linearly increase with plant inputs because the microbial processing of soil OM is also likely altered in the studied forest.

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.

Root Aliphatic Suberin Analysis Using Non-extraction or Solvent-extraction Methods

Here we describe both non-extraction and solvent-extraction methods for root aliphatic suberin analysis. The non-extraction method is fast as roots are directly depolymerized using acidic transmethylation. However, suberin aliphatic components are isolated together with all the other acyl chains making up the lipids (e.g., membranes) present in roots. For the solvent-extraction method, roots are first delipidated before transmethylation. This method is longer but allows separation of soluble and polymerized root lipids. This protocol is optimized for tissue culture- or soil-grown Arabidopsis thaliana plants, but can be used with roots of other plants.

Fatty acid ω-hydroxylases from Solanum tuberosum

Potato StCYP86A33 complements the Arabidopsis AtCYP86A1 mutant, horst - 1. Suberin is a cell-wall polymer that comprises both phenolic and aliphatic components found in specialized plant cells. Aliphatic suberin is characterized by bi-functional fatty acids, typically ω-hydroxy fatty acids and α,ω-dioic acids, which are linked via glycerol to form a three-dimensional polymer network. In potato (Solanum tuberosum L.), over 65 % of aliphatics are either ω-hydroxy fatty acids or α,ω-dioic acids. Since the biosynthesis of α,ω-dioic acids proceeds sequentially through ω-hydroxy fatty acids, the formation of ω-hydroxy fatty acids represents a significant metabolic commitment during suberin deposition. Four different plant cytochrome P450 subfamilies catalyze ω-hydroxylation, namely, 86A, 86B, 94A, and 704B; though to date, only a few members have been functionally characterized. In potato, CYP86A33 has been identified and implicated in suberin biosynthesis through reverse genetics (RNAi); however, attempts to express the CYP86A33 protein and characterize its catalytic function have been unsuccessful. Herein, we describe eight fatty acid ω-hydroxylase genes (three CYP86As, one CYP86B, three CYP94As, and a CYP704B) from potato and demonstrate their tissue expression. We also complement the Arabidopsis cyp86A1 mutant horst-1 using StCYP86A33 under the control of the Arabidopsis AtCYP86A1 promoter. Furthermore, we provide preliminary analysis of the StCYP86A33 promoter using a hairy root transformation system to monitor pStCYP86A33::GUS expression constructs. These data confirm the functional role of StCYP86A33 as a fatty acid ω-hydroxylase, and demonstrate the utility of hairy roots in the study of root-specific genes.

Lipid transfer proteins: classification, nomenclature, structure, and function

The non-specific lipid transfer proteins (LTPs) constitute a large protein family found in all land plants. They are small proteins characterized by a tunnel-like hydrophobic cavity, which makes them suitable for binding and transporting various lipids. The LTPs are abundantly expressed in most tissues. In general, they are synthesized with an N-terminal signal peptide that localizes the protein to spaces exterior to the plasma membrane. The in vivo functions of LTPs are still disputed, although evidence has accumulated for a role in the synthesis of lipid barrier polymers, such as cuticular waxes, suberin, and sporopollenin. There are also reports suggesting that LTPs are involved in signaling during pathogen attacks. LTPs are considered as key proteins for the plant's survival and colonization of land. In this review, we aim to present an overview of the current status of LTP research and also to discuss potential future applications of these proteins. We update the knowledge on 3D structures and lipid binding and review the most recent data from functional investigations, such as from knockout or overexpressing experiments. We also propose and argument for a novel system for the classification and naming of the LTPs.

Tetraploidy enhances the ability to exclude chloride from leaves in carrizo citrange seedlings

Tetraploid citrus seedlings are more tolerant to salt stress than diploid genotypes. To provide insight into the causes of differences in salt tolerance due to ploidy and thus to better understand Cl^- exclusion mechanisms in citrus, diploid and tetraploid seedlings of Carrizo citrange (CC) were grown at 0 (control) and 40mM NaCl (salt-treated) medium for 20 days. Chloride uptake and root-to-shoot translocation rates were on average 1.4-fold higher in diploid than in tetraploid salt-treated plants, which resulted in a greater (1.6-fold) Cl^- build up in the leaves of the former. Root hydraulic conductance and leaf transpiration rate were 58% and 17% lower, respectively, in tetraploid than in diploid control plants. Differences remained after salt treatment which reduced these parameters by 30-40% in both genotypes. Morphology of the root system was significantly influenced by ploidy. Tetraploid roots were less branched and with lower number of root tips than those of diploid plants. The cross-section diameter and area were lower in the diploid, and consequently specific root length was higher (1.7-fold) than in tetraploid plants. The exodermis in sections close to the root apex was broader and with higher deposition of suberin in cell walls in the tetraploid than in the diploid genotype. Net CO₂ assimilation rate in tetraploid salt-treated seedlings was 1.5-fold higher than in diploid salt-treated plants, likely due to the loss of photosynthetic capacity of diploid plants induced by Cl^- toxicity. Leaf damage was much higher, in terms of burnt area and defoliation, in diploid than in tetraploid salt-treated plants (8- and 6-fold, respectively). Salt treatment significantly reduced (37%) the dry weight of the diploid plants, but did not affect the tetraploids. In conclusion, tetraploid CC plants appear more tolerant to salinization and this effect seems mainly due to differences in morphological and histological traits of roots affecting hydraulic conductance and transpiration rate. These results may suggest that tetraploid CC used as rootstock could improve salt tolerance in citrus trees.

Ammonium-induced architectural and anatomical changes with altered suberin and lignin levels significantly change water and solute permeabilities of rice (Oryza sativa L.) roots

Non-optimal ammonium levels significantly alter root architecture, anatomy and root permeabilities for water and nutrient ions. Higher ammonium levels induced strong apoplastic barriers whereas it was opposite for lower levels. Application of nitrogen fertilizer increases crop productivity. However, non-optimal applications can have negative effects on plant growth and development. In this study, we investigated how different levels of ammonium (NH4 (+)) [low (30 or 100 μM) or optimum (300 μM) or high (1000 or 3000 μM)] affect physio-chemical properties of 1-month-old, hydroponically grown rice roots. Different NH4 (+) treatments markedly altered the root architecture and anatomy. Plants grown in low NH4 (+) had the longest roots with a weak deposition of suberised and lignified apoplastic barriers, and it was opposite for plants grown in high NH4 (+). The relative expression levels of selected suberin and lignin biosynthesis candidate genes, determined using qRT-PCR, were lowest in the roots from low NH4 (+), whereas, they were highest for those grown in high NH4 (+). This was reflected by the suberin and lignin contents, and was significantly lower in roots from low NH4 (+) resulting in greater hydraulic conductivity (Lp r) and solute permeability (P sr) than roots from optimum NH4 (+). In contrast, roots grown at high NH4 (+) had markedly greater suberin and lignin contents, which were reflected by strong barriers. These barriers significantly decreased the P sr of roots but failed to reduce the Lp r below those of roots grown in optimum NH4 (+), which can be explained in terms of the physical properties of the molecules used and the size of pores in the apoplast. It is concluded that, in rice, non-optimal NH4 (+) levels differentially affected root properties including Lp r and P sr to successfully adapt to the changing root environment.

Xylem parenchyma cell walls lack a gravitropic response in conifer compression wood

Cell wall fluorescence and immunocytochemistry demonstrate that xylem parenchyma cell walls do not show changes in structure and composition related to gravitropic response comparable to those of tracheids, even when they have lignified secondary cell walls. Tracheid cell walls in compression wood have altered composition and structure which generates the strain responsible for correction of stem lean as part of the gravitropic response of woody plants. Xylem parenchyma cell walls vary among conifer species and can be lignified secondary walls (spruce) or unlignified primary walls (pine). It can be expected that xylem parenchyma with lignified secondary cell walls might show features of compression wood comparable to those of tracheids that have a similar type of cell wall. A comparison of xylem parenchyma cell walls in normal and compression wood in species with lignified and non-lignified parenchyma cell walls provides a unique opportunity to understand the process of reaction wood formation in conifers. Using both UV/visible fluorescence microscopy of cell wall fluorophores and immunocytochemistry of galactan and mannan epitopes, we demonstrate that xylem parenchyma cell walls do not show the changes in composition and structure typical of compression wood tracheids. Adjacent cells of different types but with similar cell wall structure can undergo cell wall developmental changes related to support or defence functions independent of their neighbours. Tracheids are sensitive to gravitropic signals while xylem parenchyma cells are not.

Induction of host defences by Rhizobium during ineffective nodulation of pea (Pisum sativum L.) carrying symbiotically defective mutations sym40 (PsEFD), sym33 (PsIPD3/PsCYCLOPS) and sym42

Rhizobia are able to establish a beneficial interaction with legumes by forming a new organ, called the symbiotic root nodule, which is a unique ecological niche for rhizobial nitrogen fixation. Rhizobial infection has many similarities with pathogenic infection and induction of defence responses accompanies both interactions, but defence responses are induced to a lesser extent during rhizobial infection. However, strong defence responses may result from incompatible interactions between legumes and rhizobia due to a mutation in either macro- or microsymbiont. The aim of this research was to analyse different plant defence reactions in response to Rhizobium infection for several pea (Pisum sativum) mutants that result in ineffective symbiosis. Pea mutants were examined by histochemical and immunocytochemical analyses, light, fluorescence and transmission electron microscopy and quantitative real-time PCR gene expression analysis. It was observed that mutations in pea symbiotic genes sym33 (PsIPD3/PsCYCLOPS encoding a transcriptional factor) and sym40 (PsEFD encoding a putative negative regulator of the cytokinin response) led to suberin depositions in ineffective nodules, and in the sym42 there were callose depositions in infection thread (IT) and host cell walls. The increase in deposition of unesterified pectin in IT walls was observed for mutants in the sym33 and sym42; for mutant in the sym42, unesterified pectin was also found around degrading bacteroids. In mutants in the genes sym33 and sym40, an increase in the expression level of a gene encoding peroxidase was observed. In the genes sym40 and sym42, an increase in the expression levels of genes encoding a marker of hypersensitive reaction and PR10 protein was demonstrated. Thus, a range of plant defence responses like suberisation, callose and unesterified pectin deposition as well as activation of defence genes can be triggered by different pea single mutations that cause perception of an otherwise beneficial strain of Rhizobium as a pathogen.

Binding interactions between suberin monomer components and pesticides

Understanding the role of biomacromolecules and their interactions with pollutants is a key for elucidating the sorption mechanisms and making an accurate assessment of the environmental fate of pollutants. The knowledge of the sorption properties of the different constituents of these biomacromolecules may furnish a significant contribution to this purpose. Suberin is a very abundant biopolymer in higher plants. In this study, suberin monomers isolated from cork were analyzed by thermally-assisted methylation with tetramethylammonium hydroxide (TMAH) in a pyrolysis unit coupled to gas chromatography-mass spectrometry (GC/MS). The isolated monomer mixture was used to study the sorption of three pesticides (isoproturon, methomyl and oxamyl). The modes of pesticide-sorbent interactions were analyzed by means of two modeling calculations, the first one representing only the mixture of suberin monomers used in the sorption study, and the second one including glycerol to the mixture of suberin monomers, as a building block of the suberin molecule. The results indicated that the highest sorption capacity exhibited by the sorbent was for isoproturon (33%) being methomyl and oxamyl sorbed by the main suberin components to a lesser extent (3% and<1%, respectively). In addition to van der Waals interactions with the apolar region of sorbent and isoproturon, modeling calculations evidenced the formation of a hydrogen bond between the isoproturon NH group and a carboxylic oxygen atom of a suberin monomer. In the case of methomyl and oxamyl only weak van der Waals interactions stabilize the pesticide-sorbent adducts. The presence of glycerol in the model provoked significant changes in the interactions with isoproturon and methomyl.

Analysis of aliphatic waxes associated with root periderm or exodermis from eleven plant species

Aliphatic waxes can be found in association with suberized tissues, including roots. Non-polar lipids were isolated by rapid solvent extraction of mature regions of intact roots from eleven angiosperms, including both monocots and dicots. The majority of roots analyzed were taproots or tuberous taproots that had undergone secondary growth and thus were covered by a suberized periderm. The exceptions therein were maize (Zea mays L.) and rice (Oryza sativa L.), which present a suberized exodermis. The analysis herein focused on aliphatic waxes, with particular emphasis on alkyl hydroxycinnamates (AHCs). AHCs were widely distributed, absent from only one species, were found in both aerial and subterranean portions of tuberous taproots, and were associated with the fibrous roots of both maize and rice. Most species also contained monoacylglycerols, fatty alcohols and/or free fatty acids. Carrot (Daucus carrota L.) was the outlier, containing only free fatty acids, sterols, and polyacetylenes as identified components. Sterols were the only ubiquitous component across all roots analyzed. Monoacylglycerols of ω-hydroxy fatty acids were present in maize and rice root waxes. For species within the Brassiceae, wax compositions varied between subspecies or varieties and between aerial and subterranean portions of taproots. In addition, reduced forms of photo-oxidation products of ω-hydroxy oleate and its corresponding dicarboxylic acid (10,18-dihydroxy-octadec-8-enoate, 9,18-dihydroxy-octadec-10-enoate and 9-hydroxyoctadec-10-ene-1,18-dioate) were identified as naturally occurring suberin monomers in rutabaga (Brassica napus subsp. rapifera Metzg.) periderm tissues.