Differential induction of polar and non-polar metabolism during wound-induced suberization in potato (Solanum tuberosum L.) tubers

A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions

Plants intricately deploy defense systems to counter diverse biotic and abiotic stresses. Omics technologies, spanning genomics, transcriptomics, proteomics, and metabolomics, have revolutionized the exploration of plant defense mechanisms, unraveling molecular intricacies in response to various stressors. However, the complexity and scale of omics data necessitate sophisticated analytical tools for meaningful insights. This review delves into the application of artificial intelligence algorithms, particularly machine learning and deep learning, as promising approaches for deciphering complex omics data in plant defense research. The overview encompasses key omics techniques and addresses the challenges and limitations inherent in current AI-assisted omics approaches. Moreover, it contemplates potential future directions in this dynamic field. In summary, AI-assisted omics techniques present a robust toolkit, enabling a profound understanding of the molecular foundations of plant defense and paving the way for more effective crop protection strategies amidst climate change and emerging diseases.

Unraveling the mechanism of potato (Solanum tuberosum L.) tuber sprouting using transcriptome and metabolome analyses

Sprouting is an irreversible deterioration of potato quality, which leads to the production of harmful toxins and loss of the commercial value of potatoes. However, there is no report on the changes in different stages of potato sprouting through transcriptome and metabonomics. In this study, 1471 differentially expressed genes (DEGs) were found between DP and BP. In comparison with SP, a total of 6309 DEGs were detected in BP. Additionally, 6624 DEGs were identified between DP and SP. Moreover, 96 and 117 differentially accumulated metabolites (DAMs) were detected between DP and BP and between BP and SP, respectively. Furthermore, 130 DAMs were identified in total between DP and SP. In each group, a correlation analysis of DAMs and DEGs was performed to examine the regulatory network. The results indicated that the sprouting of tubers is mainly regulated by plant hormone signals, and during the sprouting of tubers, significant changes in metabolic products occur in the body. According to the combined analysis of transcriptomics and metabolomics, multiple metabolites were both positive and negative regulated by genes.

Wounding induces suberin deposition, relevant gene expressions and changes of endogenous phytohormones in Chinese yam (Dioscorea opposita) tubers

Wounds on Chinese yam (Dioscorea opposita ) tubers can ocurr during harvest and handling, and rapid suberisation of the wound is required to prevent pathogenic infection and desiccation. However, little is known about the causal relationship among suberin deposition, relevant gene expressions and endogenous phytohormones levels in response to wounding. In this study, the effect of wounding on phytohormones levels and the expression profiles of specific genes involved in wound-induced suberisation were determined. Wounding rapidly increased the expression levels of genes, including PAL , C4H , 4CL , POD , KCSs , FARs , CYP86A1 , CYP86B1 , GPATs , ABCGs and GELPs , which likely involved in the biosynthesis, transport and polymerisation of suberin monomers, ultimately leading to suberin deposition. Wounding induced phenolics biosynthesis and being polymerised into suberin poly(phenolics) (SPP) in advance of suberin poly(aliphatics) (SPA) accumulation. Specifically, rapid expression of genes (e.g. PAL , C4H , 4CL , POD ) associated with the biosynthesis and polymerisation of phenolics, in consistent with SPP accumulation 3days after wounding, followed by the massive accumulation of SPA and relevant gene expressions (e.g. KCSs , FARs , CYP86A1 /B1 , GPATs , ABCGs , GELPs ). Additionally, wound-induced abscisic acid (ABA) and jasmonic acid (JA) consistently correlated with suberin deposition and relevant gene expressions indicating that they might play a central role in regulating wound suberisation in yam tubers.

The combination treatment of chlorogenic acid and sodium alginate coating could accelerate the wound healing of pear fruit by promoting the metabolic pathway of phenylpropane

Water loss and microbial infection induced by mechanical injury are the main sources of harvested loss of fruits and vegetables. Plenty studies have shown that regulating phenylpropane-related metabolic pathways can effectively accelerate wound healing. The combination treatment of chlorogenic acid and sodium alginate coating on postharvest wound healing of pear fruit were investigated in this work. The result shows combination treatment reduced weight loss and disease index of the pears, enhanced texture of healing tissues, maintained the integrity of cell membrane system. Moreover, chlorogenic acid increased the content of total phenols and flavonoids, and ultimately leads to the accumulation of suberin poly phenolic (SPP) and lignin around wound cell wall. Activities of phenylalanine metabolism-related enzymes (PAL, C4H, 4CL, CAD, POD and PPO) in wound-healing tissue were enhanced. The contents of major substrates such as trans-cinnamic, p-coumaric, caffeic, and ferulic acids also increased. The presented results suggested that the combination treatment of chlorogenic acid and sodium alginate coating stimulated wound healing in pears by elevating the phenylpropanoid metabolism pathway, so that maintain high postharvest fruit quality.

Transcriptomic and metabolomic profiling reveal the mechanism underlying the inhibition of wound healing by ascorbic acid in fresh-cut potato

Ascorbic acid (AsA) inhibits wound healing in fresh-cut potatoes (FCP); however, the comprehensive regulatory mechanisms of the chemical during wound healing remain unclear. Here, physiobiochemical, transcriptomic, and metabolomic analyses were performed. In total, 685 differentially expressed genes (DEGs) and 1921 differentially accumulated metabolites (DAMs) were identified between control and AsA-treated samples. The level of the majority of DEGs expression and DAMs abundance in AsA-treated samples were similar to data of newly cut samples. The collective data indicated that the AsA treatment inhibited wound healing in FCPs by regulating glutathione metabolism, enhancing starch metabolism, and inhibiting phenylalanine metabolism, sucrose degradation, and fatty acid synthesis. Major genes and metabolites affected by AsA treatment included StGST, StPAL, StPHO1 and StLOX5, and starch, sucrose, and linoleic acid. AsA treatment increased starch content and amylase and lipoxygenase activity and decreased free fatty acid level. Our research provides fundamental insights into wound healing mechanisms in FCP.

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.

Characterization of MdMYB68, a suberin master regulator in russeted apples

INTRODUCTION

Apple russeting is mainly due to the accumulation of suberin in the cell wall in response to defects and damages in the cuticle layer. Over the last decades, massive efforts have been done to better understand the complex interplay between pathways involved in the suberization process in model plants. However, the regulation mechanisms which orchestrate this complex process are still under investigation. Our previous studies highlighted a number of transcription factor candidates from the Myeloblastosis (MYB) transcription factor family which might regulate suberization in russeted or suberized apple fruit skin. Among these, we identified MdMYB68, which was co-expressed with number of well-known key suberin biosynthesis genes.

METHOD

To validate the MdMYB68 function, we conducted an heterologous transient expression in Nicotiana benthamiana combined with whole gene expression profiling analysis (RNA-Seq), quantification of lipids and cell wall monosaccharides, and microscopy.

RESULTS

MdMYB68 overexpression is able to trigger the expression of the whole suberin biosynthesis pathway. The lipid content analysis confirmed that MdMYB68 regulates the deposition of suberin in cell walls. Furthermore, we also investigated the alteration of the non-lipid cell wall components and showed that MdMYB68 triggers a massive modification of hemicelluloses and pectins. These results were finally supported by the microscopy.

DISCUSSION

Once again, we demonstrated that the heterologous transient expression in N. benthamiana coupled with RNA-seq is a powerful and efficient tool to investigate the function of suberin related transcription factors. Here, we suggest MdMYB68 as a new regulator of the aliphatic and aromatic suberin deposition in apple fruit, and further describe, for the first time, rearrangements occurring in the carbohydrate cell wall matrix, preparing this suberin deposition.

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.

Interference Expression of StMSD Inhibited the Deposition of Suberin and Lignin at Wounds of Potato Tubers by Reducing the Production of H2O2

Superoxide dismutase (SOD) actively participates in the wound stress of plants. However, whether StMSD mediates the generation of H₂O₂ and the deposition of suberin polyphenolic and lignin at potato tuber wounds is elusive. In this study, we developed the StMSD interference expression of potato plants and tubers by Agrobacterium tumefaciens-mediated transformation. The StSOD expression showed a marked downregulation in StMSD-interference tubers, especially StCSD2 and StCSD3. The content of O₂^•− exhibited a noticeable increase together with the inhibition in H₂O₂ accumulation. Moreover, the gene expression levels of StPAL (phenylalanine ammonia-lyase) and StC4H (cinnamate-4-hydroxylase) were downregulated in StMSD-interference tubers, and less suberin polyphenolic and lignin depositions at the wounds were observed. Taken together, the interference expression of StMSD can result in less suberin polyphenolic and lignin deposition by inhibiting the disproportionation of O₂^•− to H₂O₂ and restraining phenylpropanoid metabolism in tubers.

Sodium silicate promotes wound healing by inducing the deposition of suberin polyphenolic and lignin in potato tubers

Wound healing is a postharvest characteristic of potato tubers through accumulating suberin and lignin, which could reduce decay and water loss during storage. This study aimed to explore the impact and mechanisms of sodium silicate on wound healing of potatoes. After being wounded, "Atlantic" potato tubers were treated with water or 50 mM sodium silicate. The results showed that sodium silicate treatment accelerated the formation of wound healing structures and significantly reduced the weight loss and disease index of tubers. Furthermore, sodium silicate induced the genes expression and enzyme activity of phenylalanine ammonia lyase (PAL), 4-coumarate: coenzyme A ligase (4CL), and cinnamyl alcohol dehydrogenase (CAD) involved in the phenylpropane metabolism, enhancing the synthesis of the main precursors of suberin polyphenolic (SPP) and lignin, such as coniferyl alcohol, sinapyl alcohol, and cinnamyl alcohol. Meanwhile, the gene expression of StPOD and StNOX was activated, and the production of O^2- and H₂O₂ was promoted, which could be used for injury signal transmission and oxidative crosslinking of SPP monomers and lignin precursors. Besides, antimicrobial compounds, total phenolics, and flavonoids were also induced. We suggest that sodium silicate could promote wound healing by inducing the deposition of SPP, lignin, and antimicrobial compounds in potato tubers.

The making of suberin

Outer protective barriers of animals use a variety of bio-polymers, based on either proteins (e.g. collagens), or modified sugars (e.g. chitin). Plants, however, have come up with a particular solution, based on the polymerisation of lipid-like precursors, giving rise to cutin and suberin. Suberin is a structural lipophilic polyester of fatty acids, glycerol and some aromatics found in cell walls of phellem, endodermis, exodermis, wound tissues, abscission zones, bundle sheath and other tissues. It deposits as a hydrophobic layer between the (ligno)cellulosic primary cell wall and plasma membrane. Suberin is highly protective against biotic and abiotic stresses, shows great developmental plasticity and its chemically recalcitrant nature might assist the sequestration of atmospheric carbon by plants. The aim of this review is to integrate the rapidly accelerating genetic and cell biological discoveries of recent years with the important chemical and structural contributions obtained from very diverse organisms and tissue layers. We critically discuss the order and localisation of the enzymatic machinery synthesising the presumed substrates for export and apoplastic polymerisation. We attempt to explain observed suberin linkages by diverse enzyme activities and discuss the spatiotemporal relationship of suberin with lignin and ferulates, necessary to produce a functional suberised cell wall.

Integrated Analysis of Transcriptome and Metabolome Reveals the Mechanism of Chlorine Dioxide Repressed Potato (Solanum tuberosum L.) Tuber Sprouting

Sprouting is an irreversible deterioration of potato quality, which not only causes loss in their commercial value but also produces harmful toxins. As a popular disinfectant, ClO2 can inhibit the sprouting of potato tubers. Using transcriptomic and metabolomic approaches to understand the repressive mechanism of ClO2 in potato sprouting is yet to be reported. Sequencing the transcriptome and metabolome of potatoes treated with ClO2 in this study revealed a total of 3,119 differentially expressed genes, with 1,247 and 1,872 genes showing down- and upregulated expression, respectively. The majority of the downregulated genes were associated with plant hormone signal transduction, whereas upregulated differential genes were associated primarily with biological processes, such as phenylpropanoid biosynthesis and the mitogen-activated protein kinase (MAPK) signaling pathway. Metabonomic assays identified a total of 932 metabolites, with 33 and 52 metabolites being down- and upregulated, respectively. Downregulated metabolites were mostly alkaloids, amino acids, and their derivatives, whereas upregulated metabolites were composed mainly of flavonoids and coumarins. Integrated transcriptomic and metabolomic analyses showed that many different metabolites were regulated by several different genes, forming a complex regulatory network. These results provide new insights for understanding the mechanism of ClO2-mediated repression of potato sprouting.

Chemical and Molecular Characterization of Wound-Induced Suberization in Poplar (Populus alba × P. tremula) Stem Bark

Upon mechanical damage, plants produce wound responses to protect internal tissues from infections and desiccation. Suberin, a heteropolymer found on the inner face of primary cell walls, is deposited in specific tissues under normal development, enhanced under abiotic stress conditions and synthesized by any tissue upon mechanical damage. Wound-healing suberization of tree bark has been investigated at the anatomical level but very little is known about the molecular mechanisms underlying this important stress response. Here, we investigated a time course of wound-induced suberization in poplar bark. Microscopic changes showed that polyphenolics accumulate 3 days post wounding, with aliphatic suberin deposition observed 5 days post wounding. A wound periderm was formed 9 days post wounding. Chemical analyses of the suberin polyester accumulated during the wound-healing response indicated that suberin monomers increased from 0.25 to 7.98 mg/g DW for days 0 to 28, respectively. Monomer proportions varied across the wound-healing process, with an overall ratio of 2:1 (monomers:glycerol) found across the first 14 days post wounding, with this ratio increasing to 7:2 by day 28. The expression of selected candidate genes of poplar suberin metabolism was investigated using qRT-PCR. Genes queried belonging to lipid polyester and phenylpropanoid metabolism appeared to have redundant functions in native and wound-induced suberization. Our data show that, anatomically, the wounding response in poplar bark is similar to that described in periderms of other species. It also provides novel insight into this process at the chemical and molecular levels, which have not been previously studied in trees.

Transcriptome sequencing and differential expression analysis of natural and BTH-treated wound healing in potato tubers (Solanum tuberosum L.)

Background

Wound healing is a representative phenomenon of potato tubers subjected to mechanical injuries. Our previous results found that benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) promoted the wound healing of potato tubers. However, the molecular mechanism related to inducible wound healing remains unknown.

Results

Transcriptomic evaluation of healing tissues from potato tubers at three stages, namely, 0 d (nonhealing), 5 d (wounded tubers healed for 5 d) and 5 d (BTH-treated tubers healed for 5 d) using RNA-Seq and differentially expressed genes (DEGs) analysis showed that more than 515 million high-quality reads were generated and a total of 7665 DEGs were enriched, and 16 of these DEGs were selected by qRT-PCR analysis to further confirm the RNA sequencing data. Gene ontology (GO) enrichment analysis indicated that the most highly DEGs were involved in metabolic and cellular processes, and KEGG enrichment analysis indicated that a large number of DEGs were associated with plant hormones, starch and sugar metabolism, fatty acid metabolism, phenylpropanoid biosynthesis and terpenoid skeleton biosynthesis. Furthermore, a few candidate transcription factors, including MYB, NAC and WRKY, and genes related to Ca²⁺-mediated signal transduction were also found to be differentially expressed during wound healing. Most of these enriched DEGs were upregulated after BTH treatment.

Conclusion

This comparative expression profile provided useful resources for studies of the molecular mechanism via these promising candidates involved in natural or elicitor-induced wound healing in potato tubers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08480-1.

Brassinosteroid Accelerates Wound Healing of Potato Tubers by Activation of Reactive Oxygen Metabolism and Phenylpropanoid Metabolism

Wound healing could effectively reduce the decay rate of potato tubers after harvest, but it took a long time to form typical and complete healing structures. Brassinosteroid (BR), as a sterol hormone, is important for enhancing plant resistance to abiotic and biotic stresses. However, it has not been reported that if BR affects wound healing of potato tubers. In the present study, we observed that BR played a positive role in the accumulation of lignin and suberin polyphenolic (SPP) at the wounds, and effectively reduced the weight loss and disease index of potato tubers (cv. Atlantic) during healing. At the end of healing, the weight loss and disease index of BR group was 30.8% and 23.1% lower than the control, respectively. Furthermore, BR activated the expression of StPAL, St4CL, StCAD genes and related enzyme activities in phenylpropanoid metabolism, and promoted the synthesis of lignin precursors and phenolic acids at the wound site, mainly by inducing the synthesis of caffeic acid, sinapic acid and cinnamyl alcohol. Meanwhile, the expression of StNOX was induced and the production of O²⁻ and H₂O₂ was promoted, which mediated oxidative crosslinking of above phenolic acids and lignin precursors to form SPP and lignin. In addition, the expression level of StPOD was partially increased. In contrast, the inhibitor brassinazole inhibited phenylpropanoid metabolism and reactive oxygen metabolism, and demonstrated the function of BR hormone in healing in reverse. Taken together, the activation of reactive oxygen metabolism and phenylpropanoid metabolism by BR could accelerate the wound healing of potato tubers.

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 is required for exodermal suberization to form a barrier to radial oxygen loss in the adventitious roots of rice (Oryza sativa)

To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice.

Effect of Polystyrene Microplastics on Rice Seed Germination and Antioxidant Enzyme Activity

The accumulation and distribution of microplastics (MPs) in agricultural soils, including rice fields, is well studied. However, only a few studies have investigated the uptake of MPs by rice plants and the consequential toxic effects of MPs under solid-phase culture conditions. Hence, in this study, we explored the effects of different concentrations of polystyrene MPs (PS-MPs, with a size of 200 nm) on rice seed germination, root growth, antioxidant enzyme activity, and transcriptome. PS-MPs exhibited no significant effect on the germination of rice seeds (p > 0.05). However, PS-MPs significantly promoted root length (10 mg L⁻¹; p < 0.05), and significantly reduced antioxidant enzyme activity (1000 mg L⁻¹; p < 0.05). Staining with 3,3-diaminobenzidine and nitrotetrazolium blue chloride further revealed significant accumulation of reactive oxygen species in the roots of rice treated with PS-MPs. In addition, transcriptome data analysis revealed that PS-MPs induce the expression of genes related to antioxidant enzyme activity in plant roots. Specifically, genes related to flavonoid and flavonol biosynthesis were upregulated, whereas those involved in linolenic acid and nitrogen metabolism were downregulated. These results enhance our understanding of the responses of agricultural crops to MP toxicity.

Transcriptional regulation of wound suberin deposition in potato cultivars with differential wound healing capacity

Wounding during mechanical harvesting and post-harvest handling results in tuber desiccation and provides an entry point for pathogens resulting in substantial post​-harvest crop losses. Poor wound healing is a major culprit of these losses. Wound tissue in potato (Solanum tuberosum) tubers, and all higher plants, is composed of a large proportion of suberin that is deposited in a specialized tissue called the wound periderm. However, the genetic regulatory pathway controlling wound-induced suberization remains unknown. Here, we implicate two potato transcription factors, StMYB102 (PGSC0003DMG400011250) and StMYB74 (PGSC0003DMG400022399), as regulators of wound suberin biosynthesis and deposition. Using targeted metabolomics and transcript profiling from the wound healing tissues of two commercial potato cultivars, as well as heterologous expression, we provide evidence for the molecular-genetic basis of the differential wound suberization capacities of different potato cultivars. Our results suggest that (i) the export of suberin from the cytosol to the apoplast and ligno-suberin deposition may be limiting factors for wound suberization, (ii) StMYB74 and StMYB102 are important regulators of the wound suberization process in tubers, and (iii) polymorphisms in StMYB102 may influence cultivar-specific wound suberization capacity. These results represent an important step in understanding the regulated biosynthesis and deposition of wound suberin and provide a practical foundation for targeted breeding approaches aimed at improving potato tuber storage life.

Candida Oleophila Proliferated and Accelerated Accumulation of Suberin Poly Phenolic and Lignin at Wound Sites of Potato Tubers

Candida oleophila is a type of biocontrol yeast offering effective postharvest disease control. To the best of our knowledge, the effect of C. oleophila upon the healing of tubers is yet to be studied. The present study addresses the existing knowledge gap by investigating the effect of C. oleophila on wound healing in potato tubers. The results show that C. oleophila colonized and proliferated at the wound sites during the early and intermediate stages of healing. In addition, C. oleophila reduced weight loss of wounded tubers, decreased disease index of inoculated tubers with Fusarium sulphureum, and accelerated accumulation of suberin poly phenolic (SPP) and lignin at wound sites. C. oleophila activated phenylpropanoid metabolism and increased the content of SPP monomers, total phenol, flavonoids, and lignin. Furthermore, the yeast increased H₂O₂ content as well as peroxidase activity.

BdFAR4, a root-specific fatty acyl-coenzyme A reductase, is involved in fatty alcohol synthesis of root suberin polyester in Brachypodium distachyon

Suberin is a complex hydrophobic polymer of aliphatic and phenolic compounds which controls the movement of gases, water, and solutes and protects plants from environmental stresses and pathogenic infection. The synthesis and regulatory pathways of suberin remain unknown in Brachypodium distachyon. Here we describe the identification of a B. distachyon gene, BdFAR4, encoding a fatty acyl-coenzyme A reductase (FAR) by a reverse genetic approach, and investigate the molecular relevance of BdFAR4 in the root suberin synthesis of B. distachyon. BdFAR4 is specifically expressed throughout root development. Heterologous expression of BdFAR4 in yeast (Saccharomyces cerevisiae) afforded the production of C20:0 and C22:0 fatty alcohols. The loss-of-function knockout of BdFAR4 by CRISPR/Cas9-mediated gene editing significantly reduced the content of C20:0 and C22:0 fatty alcohols associated with root suberin. In contrast, overexpression of BdFAR4 in B. distachyon and tomato (Solanum lycopersicum) resulted in the accumulation of root suberin-associated C20:0 and C22:0 fatty alcohols, suggesting that BdFAR4 preferentially accepts C20:0 and C22:0 fatty acyl-CoAs as substrates. The BdFAR4 protein was localized to the endoplasmic reticulum in Arabidopsis thaliana protoplasts and Nicotiana benthamiana leaf epidermal cells. BdFAR4 transcript levels can be increased by abiotic stresses and abscisic acid treatment. Furthermore, yeast one-hybrid, dual-luciferase activity, and electrophoretic mobility shift assays indicated that the R2R3-MYB transcription factor BdMYB41 directly binds to the promoter of BdFAR4. Taken together, these results imply that BdFAR4 is essential for the production of root suberin-associated fatty alcohols, especially under stress conditions, and that its activity is transcriptionally regulated by the BdMYB41 transcription factor.

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.

Blocking intruders: inducible physico-chemical barriers against plant vascular wilt pathogens

Xylem vascular wilt pathogens cause devastating diseases in plants. Proliferation of these pathogens in the xylem causes massive disruption of water and mineral transport, resulting in severe wilting and death of the infected plants. Upon reaching the xylem vascular tissue, these pathogens multiply profusely, spreading vertically within the xylem sap, and horizontally between vessels and to the surrounding tissues. Plant resistance to these pathogens is very complex. One of the most effective defense responses in resistant plants is the formation of physico-chemical barriers in the xylem tissue. Vertical spread within the vessel lumen is restricted by structural barriers, namely, tyloses and gels. Horizontal spread to the apoplast and surrounding healthy vessels and tissues is prevented by vascular coating of the colonized vessels with lignin and suberin. Both vertical and horizontal barriers compartmentalize the pathogen at the infection site and contribute to their elimination. Induction of these defenses are tightly coordinated, both temporally and spatially, to avoid detrimental consequences such as cavitation and embolism. We discuss current knowledge on mechanisms underlying plant-inducible structural barriers against major xylem-colonizing pathogens. This knowledge may be applied to engineer metabolic pathways of vascular coating compounds in specific cells, to produce plants resistant towards xylem colonizers.

Postharvest benzothiazole treatment enhances healing in mechanically damaged sweet potato by activating the phenylpropanoid metabolism

BACKGROUND

Sweet potato often suffers mechanical damage during harvest, handling, and transportation. Infections, water loss, and quality changes of sweet potato caused by mechanical damage pose great financial losses. Wound healing is an effective method to alleviate such problems. In this study, the effects of postharvest treatment with benzothiazole (BTH) on wound healing of sweet potato was investigated.

RESULTS

Postharvest BTH treatment of sweet potatoes promoted lignin accumulation in wounded tissues, and 100 mg L^-1 BTH exhibited better effects than 50 mg L^-1 or 150 mg L^-1 BTH. The biosynthesis of lignin in wounded tissues significantly decreased the weight loss of sweet potatoes. An increase in respiration intensity after BTH treatment was observed. The total phenolic and flavonoid contents and the activity of phenylalanine ammonia-lyase, peroxidase, and polyphenol oxidase were increased in BTH-treated sweet potatoes. This suggests that BTH increases phenylpropanoid metabolism.

CONCLUSION

Postharvest 100 mg L^-1 BTH treatment could promote wound healing in mechanically damaged sweet potatoes. The activation of the phenylpropanoid metabolism might be the mechanism of action of BTH in wound healing. © 2020 Society of Chemical Industry.

SUBERMAN regulates developmental suberization of the Arabidopsis root endodermis

Root endodermis, the innermost cortical layer surrounding the root vasculature, serves as the foremost barrier to water, solutes, and nutrients taken up from soil. Endodermis barrier functionality is achieved via its hydrophobic coating of lignified Casparian strips and the suberin lamellae; nonetheless the regulatory mechanisms underlying endodermis suberization are still elusive. Here, we discovered that the Arabidopsis SUBERMAN (SUB) transcription factor controls the establishment of the root suberin lamellae. Transient expression of SUB in Nicotiana benthamiana leaves resulted in the induction of heterologous suberin genes, the accumulation of suberin-type monomers, and consequent deposition of suberin-like lamellae. We demonstrate that SUB exerts its regulatory roles by transactivating promoters of suberin genes. In Arabidopsis, SUB is expressed in patchy and continuous suberization root endodermal cells, and thus roots with higher or lower expression of SUB display altered suberin polymer deposition patterns and modified composition. While these changes did not interfere with Casparian strip formation they had a substantial effect on root uptake capacity, resulting in varied root and leaf ionomic phenotypes. Gene expression profiling revealed that SUB function impacts transcriptional networks associated with suberin, phenylpropanoids, lignin, and cuticular lipid biosynthesis, as well as root transport activities, hormone signalling, and cell wall modification. Our findings highlight SUB as a regulator of root endodermis suberization during normal development, and its characterization is thus a key step towards dissecting the molecular mechanisms partaking in root endodermal barrier functionalities.

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.