Very-long-chain fatty acids are involved in polar auxin transport and developmental patterning in Arabidopsis

VAP27-1 interacts with KCS6 and CER2 to facilitate the biosynthesis of very- long-chain fatty acids

Cuticular wax is primarily composed of very-long-chain fatty acids (VLCFAs) and their derivatives. It forms a critical hydrophobic layer on plant surfaces, acting as a protective barrier against biotic and abiotic stress. The biosynthesis of VLCFAs and their derivative wax occurs in endoplasmic reticulum (ER) and is subsequently transported to the plant surface. While substantial research has focused on cuticular wax biosynthesis enzymes and their transcriptional regulation, the mechanisms by which these enzymes are modulated by proteins within cytosol organelles remain poorly understood. In this study, we identified that β-ketoacyl-CoA synthase 6 (KCS6), an ER-localized rate-limiting enzyme in VLCFAs biosynthesis, also localized at ER-plasma membrane contact sites (EPCS). We further demonstrated that KCS6 and its cofactor ECERIFERUM 2 (CER2) interact with vesicle-associated membrane protein-associated protein 27-1 (VAP27-1), a key regulator of EPCS formation and stabilization. Overexpression of VAP27-1 in Arabidopsis thaliana resulted in a significant increase in almost all cuticular wax components compared to WT. Additionally, firefly luciferase complementation imaging assays (LCI) and yeast heterologous expression analysis revealed that VAP27-1 strengthens the interaction between the KCS6-CER2 complex, resulting in increased accumulation of VLCFAs. In conclusion, this study emphasized the critical role of VAP27-1 in regulating the biosynthesis of cuticular wax mediated by KCS6-CER2, providing new insights into the fine-tuning mechanisms of cuticular wax biosynthesis within the ER. Furthermore, the identification of VAP27-1 as a novel modulator of VLCFA synthases offers a potential target for enhancing plant resilience to environmental stresses.

NAM and CUC3 boundary genes maintain shoot apical meristem viability and suppress the development of axillary shoot in rice seedlings

Cell division and differentiation within the shoot apical meristem (SAM) are essential for the morphogenesis of aboveground plant organs. This study reveals that the boundary genes OsNAM and OsCUC3 collaboratively maintain SAM activity. Loss of function in both OsNAM and OsCUC3 during the fourth leaf stage reduced SAM size, with the osnam oscuc3 mutant exhibiting abnormal leaf number and morphology. Furthermore, OsNAM and OsCUC3 inhibited the growth of axillary shoots. In the osnam oscuc3 mutant, the number of new leaves decreased, while buds in the coleoptile and the axil of the first leaf developed into tillers. Since OsNAM and OsCUC3 are involved in regulating both SAM activity and the growth of lateral shoots, we examined their expression patterns at the base of the main shoot. β-Glucuronidase (GUS) reporter activity and GFP reporter lines demonstrated that OsNAM and OsCUC3 have distinct expression patterns. Specifically, OsNAM was expressed throughout the SAM, whereas OsCUC3 was expressed only at the base of the SAM, with its expression gradually decreasing as seedlings develop. RNA sequencing analysis showed that the expression of genes related to leaf epidermal cell development, cell wall components, and hormonal signal transduction was altered in response to the loss of function of OsNAM and OsCUC3. Therefore, the boundary genes OsNAM and OsCUC3 not only inhibit the growth of axillary shoots but also regulate the development of aboveground organs, including leaf morphology and number, by maintaining the SAM activity in the main shoot.

Acetyl-CoA Carboxylase1 influences ECERIFERUM2 activity to mediate the synthesis of very-long-chain fatty acid past C28

Cuticular wax is a protective layer on the aerial surfaces of land plants. In Arabidopsis (Arabidopsis thaliana), cuticular wax is mainly constituted of compounds derived from very-long-chain fatty acids (VLCFAs) with chain lengths longer than C28. CER2-LIKE (ECERIFERUM2-LIKE) proteins interact with CER6/KCS6 (ECERIFERUM6/β-Ketoacyl-CoA Synthase6), the key enzyme of the fatty acid elongase complex, to modify its substrate specificity for VLCFA elongation past C28. However, the molecular regulatory mechanism of CER2-LIKE proteins remains unclear. Arabidopsis eceriferum19 (cer19) mutants display wax-deficient stems caused by loss of waxes longer than C28, indicating that CER19 may participate in the CER2-LIKE-mediated VLCFA elongation past C28. Using positional cloning and genetic complementation, we showed that CER19 encodes Acetyl-CoA Carboxylase1 (ACC1), which catalyzes the synthesis of malonyl-CoA, the essential substrate for the CER6/KCS6-mediated condensation reaction in VLCFA synthesis. We demonstrated that ACC1 physically interacts with CER2-LIKE proteins via split-ubiquitin yeast 2-hybrid and firefly luciferase complementation imaging analysis. Additionally, heterologous expression in yeast and genetic analysis in Arabidopsis revealed that ACC1 affects CER2 activity to influence VLCFA elongation past C28. These findings imply that CER2-LIKE proteins might function as a link between ACC1 and CER6/KCS6 and subsequently enhance CER6/KCS6 binding to malonyl-CoA for further utilization in VLCFA elongation past C28. This information deepens our understanding of the complex mechanism of cuticular wax biosynthesis.

3-ketoacyl-CoA synthase 19 contributes to the biosynthesis of seed lipids and cuticular wax in Arabidopsis and abiotic stress tolerance

Very-long-chain fatty acids (VLCFAs) are essential precursors for plant membrane lipids, cuticular waxes, suberin, and storage oils. Integral to the fatty acid elongase (FAE) complex, 3-ketoacyl-CoA synthases (KCSs) function as crucial enzymes in the VLCFA pathway, determining the chain length of VLCFA. This study explores the in-planta role of the KCS19 gene. KCS19 is predominantly expressed in leaves and stem epidermis, sepals, styles, early silique walls, beaks, pedicels, and mature embryos. Localized in the endoplasmic reticulum, KCS19 interacts with other FAE proteins. kcs19 knockout mutants displayed reduced total wax and wax crystals, particularly alkanes, while KCS19 overexpression increased these components and wax crystals. Moreover, the cuticle permeability was higher for the kcs19 mutants compared to the wild type, rendering them more susceptible to drought and salt stress, whereas KCS19 overexpression enhanced drought and salt tolerance. Disrupting KCS19 increased C18 species and decreased C20 and longer species in seed fatty acids, indicating its role in elongating C18 to C20 VLCFAs, potentially up to C24 for seed storage lipids. Collectively, KCS19-mediated VLCFA synthesis is required for cuticular wax biosynthesis and seed storage lipids, impacting plant responses to abiotic stress.

Regulation of Rice Grain Weight by Fatty Acid Composition: Unveiling the Mechanistic Roles of OsLIN6 by OsARF12

Fatty acids play a putative role as second messengers of phytohormones and regulate the rice grain weight. However, the inner mechanism is still unclear and needs to be further studied. In this study, we identified that oleic acid (C18:1) negatively correlates while linoleic acid (C18:2) positively correlates with rice grain weight. Field trials showed that 1000-grain weight was significantly reduced when treated with the fatty acid synthesis inhibitor, Firsocostat S enantiomer (FSE), at the heading and flowering stages. RNA-seq analysis revealed that FSE affects grain weight by modulating processes, such as glycolysis, sucrose metabolism, and hormone signaling. Notably, FSE inhibited the expression of OsLIN6, which is responsible for transporting C18:1 to the phosphatidylcholine pool for C18:2 synthesis. Compared with the wild type (WT), the OsLIN6 knockout mutant exhibited a lower grain weight, an increased C18:1 content, and a decreased C18:2 content. Importantly, OsARF12 was shown to bind to the OsLIN6 promoter and activate its expression. In summary, this study highlights the crucial role of the fatty acid synthesis gene, OsLIN6, which was regulated by OsARF12, in rice grain weight determination, thus establishing the molecular link between fatty acid synthesis and auxin signaling.

Dynamic changes of fatty acids and (R)-dichlorprop toxicity in Arabidopsis thaliana: correlation, mechanism, and implications

Plant fatty acids (FAs) are critical components of lipids and play an important role in coping with pollution-induced stress. However, the relationship between the fluctuating changes of FAs and the toxic effects of pollutants is not clear. Here, we analyzed and identified 19 FAs, namely 14 medium and long chain fatty acids (MLCFAs) and 5 very long chain fatty acids (VLCFAs). First, a positive correlation between plant biomass and LCFA content was observed. Changes in unsaturation were inversely related to cell membrane permeability, which serves as an indicator of the toxic effects. In particular, the use of herbicides led to a reduction in total FA content, but caused a significant increase in free fatty acids (FFAs), which facilitate oxidative stress. In addition, supplementation with exogenous FAs, particularly linoleic and alpha-linolenic acids, effectively alleviated the toxic inhibition. (R)-dichlorprop causes abnormal FA metabolism that can be reversed by ferrostatin-1, a ferroptosis inhibitor. Under (R)-dichlorprop exposure, the balance of FA unsaturation in plants is disrupted by inhibition of FA desaturase activity, ultimately leading to ferroptosis and disruption of cell membrane integrity. This study aims to enhance the understanding of the ecotoxic effects of herbicides by examining changes in FAs. The findings will provide a scientific basis for controlling environmental risks associated with hazardous substances.

Comparative Transcriptomic and Lipidomic Analysis of Fatty Acid Accumulation in Three Camellia oleifera Varieties During Seed Maturing

Camellia oleifera, a major woody oil crop in China, produces tea oil rich in unsaturated fatty acids, earning it names like liquid gold and eastern olive oil. This study provides an integrated investigation of the transcriptome and lipidome within seeds at the maturing process across three C. oleifera varieties, revealing a significant relationship between fatty acid production and genes involved in lipid synthesis. Through transcriptomic analysis, 26,344 genes with varied expression were found. Functional enrichment analysis highlighted that pathways related to starch and sucrose metabolism, plant hormone signal transduction, and lipid accumulation were highly enriched among the differentially expressed genes. Coordinated high expression of key genes (ACCase, KAS I, KAS II, KAS III, KAR, HAD, EAR, SAD, LPAAT, LACS, DGAT, PDAT) during the late maturation stage contributes largely to high oil content. Additionally, expression variations of SAD and FADs among different varieties were explored. The analysis suggests that high expression of genes such as FAD3, FAD7, and FAD8 notably increased linolenic acid content. This research provides new insights into the molecular mechanisms of oil biosynthesis in C. oleifera, offering valuable references for improving yield and quality.

The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development

The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.

Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.

Tetracosanoic acids produced by 3-ketoacyl-CoA synthase 17 are required for synthesizing seed coat suberin in Arabidopsis

Very long-chain fatty acids (VLCFAs) are precursors for the synthesis of membrane lipids, cuticular waxes, suberins, and storage oils in plants. 3-Ketoacyl CoA synthase (KCS) catalyzes the condensation of C2 units from malonyl-CoA to acyl-CoA, the first rate-limiting step in VLCFA synthesis. In this study, we revealed that Arabidopsis KCS17 catalyzes the elongation of C22-C24 VLCFAs required for synthesizing seed coat suberin. Histochemical analysis of Arabidopsis plants expressing GUS (β-glucuronidase) under the control of the KCS17 promoter revealed predominant GUS expression in seed coats, petals, stigma, and developing pollen. The expression of KCS17:eYFP (enhanced yellow fluorescent protein) driven by the KCS17 promoter was observed in the outer integument1 of Arabidopsis seed coats. The KCS17:eYFP signal was detected in the endoplasmic reticulum of tobacco epidermal cells. The levels of C22 VLCFAs and their derivatives, primary alcohols, α,ω-alkane diols, ω-hydroxy fatty acids, and α,ω-dicarboxylic acids increased by ~2-fold, but those of C24 VLCFAs, ω-hydroxy fatty acids, and α,ω-dicarboxylic acids were reduced by half in kcs17-1 and kcs17-2 seed coats relative to the wild type (WT). The seed coat of kcs17 displayed decreased autofluorescence under UV and increased permeability to tetrazolium salt compared with the WT. Seed germination and seedling establishment of kcs17 were more delayed by salt and osmotic stress treatments than the WT. KCS17 formed homo- and hetero-interactions with KCR1, PAS2, and ECR, but not with PAS1. Therefore, KCS17-mediated VLCFA synthesis is required for suberin layer formation in Arabidopsis seed coats.

A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance

BACKGROUND

The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance.

RESULTS

In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified.

CONCLUSIONS

We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.

OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia

Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accommodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signaling pathway that activates 2 coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defense-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordium form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.

A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis

Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.

Protein interactomes for plant lipid biosynthesis and their biotechnological applications

Plant lipids have essential biological roles in plant development and stress responses through their functions in cell membrane formation, energy storage and signalling. Vegetable oil, which is composed mainly of the storage lipid triacylglycerol, also has important applications in food, biofuel and oleochemical industries. Lipid biosynthesis occurs in multiple subcellular compartments and involves the coordinated action of various pathways. Although biochemical and molecular biology research over the last few decades has identified many proteins associated with lipid metabolism, our current understanding of the dynamic protein interactomes involved in lipid biosynthesis, modification and channelling is limited. This review examines advances in the identification and characterization of protein interactomes involved in plant lipid biosynthesis, with a focus on protein complexes consisting of different subunits for sequential reactions such as those in fatty acid biosynthesis and modification, as well as transient or dynamic interactomes formed from enzymes in cooperative pathways such as assemblies of membrane-bound enzymes for triacylglycerol biosynthesis. We also showcase a selection of representative protein interactome structures predicted using AlphaFold2, and discuss current and prospective strategies involving the use of interactome knowledge in plant lipid biotechnology. Finally, unresolved questions in this research area and possible approaches to address them are also discussed.

Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development

Introduction

Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels.

Methods

Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes.

Results

Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers.

Discussion

Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.

Lipids and volatile organic compounds in sesame seeds and their relationships with environmental temperature-induced stress

Sesame seeds contain several lipids and fragrances that offer health benefits. However, no studies have reported a relationship between the lipids or flavor compounds of sesame seeds and environmental factors. In this study, we aimed to identify this relationship by analyzing the contents of lipidic and flavor compounds in fifteen genotypes of sesame seeds grown in two cultivation regions (Jeonju and Miryang) and years (2018 and 2019). Herein, 17 lipids and 62 flavor compounds were detected. Multivariate statistical analyses revealed that the cultivation year had a larger influence on the contents of lipidic and flavor compounds than the cultivation region and genotype. Furthermore, heat stress due to high cultivation temperature in 2018 caused the accumulation of sugar and secondary metabolites, increased flavor-related substances, and inhibited the degradation of fatty acids. Our study is the first to demonstrate the metabolic changes in lipids and flavor components of sesame in response to environmental temperature changes affected by different cultivation years. Therefore, this study provides guidance for the cultivation of commercially advantageous sesame seeds in improving the quality of sesame seeds and their products.

Harnessing enzyme cofactors and plant metabolism: an essential partnership

Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.

Roles of very long-chain fatty acids in compound leaf patterning in Medicago truncatula

Plant cuticles are composed of hydrophobic cuticular waxes and cutin. Very long-chain fatty acids (VLCFAs) are components of epidermal waxes and the plasma membrane and are involved in organ morphogenesis. By screening a barrelclover (Medicago truncatula) mutant population tagged by the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified two types of mutants with unopened flower phenotypes, named unopened flower1 (uof1) and uof2. Both UOF1 and UOF2 encode enzymes that are involved in the biosynthesis of VLCFAs and cuticular wax. Comparative analysis of the mutants indicated that the mutation in UOF1, but not UOF2, leads to the increased number of leaflets in M. truncatula. UOF1 was specifically expressed in the outermost cell layer (L1) of the shoot apical meristem (SAM) and leaf primordia. The uof1 mutants displayed defects in VLCFA-mediated plasma membrane integrity, resulting in the disordered localization of the PIN-FORMED1 (PIN1) ortholog SMOOTH LEAF MARGIN1 (SLM1) in M. truncatula. Our work demonstrates that the UOF1-mediated biosynthesis of VLCFAs in L1 is critical for compound leaf patterning, which is associated with the polarization of the auxin efflux carrier in M. truncatula.

Tackling functional redundancy of Arabidopsis fatty acid elongase complexes

Very-long-chain fatty acids (VLCFA) are precursors for various lipids playing important physiological and structural roles in plants. Throughout plant tissues, VLCFA are present in multiple lipid classes essential for membrane homeostasis, and also stored in triacylglycerols. VLCFA and their derivatives are also highly abundant in lipid barriers, such as cuticular waxes in aerial epidermal cells and suberin monomers in roots. VLCFA are produced by the fatty acid elongase (FAE), which is an integral endoplasmic reticulum membrane multi-enzymatic complex consisting of four core enzymes. The 3-ketoacyl-CoA synthase (KCS) catalyzes the first reaction of the elongation and determines the chain-length substrate specificity of each elongation cycle, whereas the other three enzymes have broad substrate specificities and are shared by all FAE complexes. Consistent with the co-existence of multiple FAE complexes, performing sequential and/or parallel reactions to produce the broad chain-length-range of VLCFA found in plants, twenty-one KCS genes have been identified in the genome of Arabidopsis thaliana. Using CRISPR-Cas9 technology, we established an expression platform to reconstitute the different Arabidopsis FAE complexes in yeast. The VLCFA produced in these yeast strains were analyzed in detail to characterize the substrate specificity of all KCS candidates. Additionally, Arabidopsis candidate proteins were transiently expressed in Nicotiana benthamiana leaves to explore their activity and localization in planta. This work sheds light on the genetic and biochemical redundancy of fatty acid elongation in plants.

New Paradigms in Brassinosteroids, Strigolactones, Sphingolipids, and Nitric Oxide Interaction in the Control of Lateral and Adventitious Root Formation

The root system is formed by the primary root (PR), which forms lateral roots (LRs) and, in some cases, adventitious roots (ARs), which in turn may produce their own LRs. The formation of ARs is also essential for vegetative propagation in planta and in vitro and for breeding programs. Root formation and branching is coordinated by a complex developmental network, which maximizes the plant's ability to cope with abiotic stress. Rooting is also a response caused in a cutting by wounding and disconnection from the donor plant. Brassinosteroids (BRs) are steroid molecules perceived at the cell surface. They act as plant-growth-regulators (PGRs) and modulate plant development to provide stress tolerance. BRs and auxins control the formation of LRs and ARs. The auxin/BR interaction involves other PGRs and compounds, such as nitric oxide (NO), strigolactones (SLs), and sphingolipids (SPLs). The roles of these interactions in root formation and plasticity are still to be discovered. SLs are carotenoid derived PGRs. SLs enhance/reduce LR/AR formation depending on species and culture conditions. These PGRs possibly crosstalk with BRs. SPLs form domains with sterols within cellular membranes. Both SLs and SPLs participate in plant development and stress responses. SPLs are determinant for auxin cell-trafficking, which is essential for the formation of LRs/ARs in planta and in in vitro systems. Although little is known about the transport, trafficking, and signaling of SPLs, they seem to interact with BRs and SLs in regulating root-system growth. Here, we review the literature on BRs as modulators of LR and AR formation, as well as their crosstalk with SLs and SPLs through NO signaling. Knowledge on the control of rooting by these non-classical PGRs can help in improving crop productivity and enhancing AR-response from cuttings.

A very-long-chain fatty acid synthesis gene, SD38, influences plant height by activating ethylene biosynthesis in rice

As an important trait in crop breeding, plant height is associated with lodging resistance and yield. With the identification and cloning of several semi-dwarfing genes, increasing numbers of semi-dwarf cultivars have emerged, which has led to a 'green revolution' in rice (Oryza sativa) production. In this study, we identified a rice semi-dwarf mutant, semi-dwarf 38 (sd38), which showed significantly reduced cell length. SD38 encodes a fatty acid elongase, β-ketoacyl-CoA synthase, which is involved in the synthesis of very-long-chain fatty acids (VLCFAs). Expression analysis showed that SD38 was localized on the membrane of the endoplasmic reticulum, and was expressed in all analyzed tissues with differential abundance. The mutation of SD38 affected lipid metabolism in the sd38 mutant. A functional complementarity test in Saccharomyces cerevisiae indicated that SD38 was capable of complementing the deficiency of ELO3p activity in BY4741-elo3 knockout yeast cells by participating in the synthesis of C24:0 VLCFA. Significant changes were observed in the expression of genes involved in ethylene synthesis, which resulted in reduced content of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the sd38 mutant. Exogenously supplied VLCFA (C24:0) increased the expression levels of OsACS3, OsACS4, and OsACO7 and the plant height of sd38 mutant seedlings, similar to the effect of exogenous application of ACC and ethephon. These results reveal a relationship among VLCFAs, ethylene biosynthesis, and plant height and improve our understanding of plant height development in crops.

Evolution and molecular basis of substrate specificity in a 3-ketoacyl-CoA synthase gene cluster from Populus trichocarpa

Very-long-chain fatty acids (VLCFAs) are precursors to sphingolipids, glycerophospholipids, and plant cuticular waxes. In plants, members of a large 3-ketoacyl-CoA synthase (KCS) gene family catalyze the substrate-specific elongation of VLCFAs. Although it is well understood that KCSs have evolved to use diverse substrates, the underlying molecular determinants of their specificity are still unclear. In this study, we exploited the sequence similarity of a KCS gene cluster from Populus trichocarpa to examine the evolution and molecular determinants of KCS substrate specificity. Functional characterization of five members (PtKCS1, 2, 4, 8, 9) in yeast showed divergent product profiles based on VLCFA length, saturation, and position of the double bond. In addition, homology models, rationally designed chimeras, and site-directed mutants were used to identify two key regions (helix-4 and position 277) as being major determinants of substrate specificity. These results were corroborated with chimeras involving a more distantly related KCS, PtCER6 (the poplar ortholog of the Arabidopsis CER6), and used to show that helix-4 is necessary for the modulatory effect of PtCER2-like 5 on KCS substrate specificity. The role of position 277 in limiting product length was further tested by substitution with smaller amino acids, which shifted specificity towards longer products. Finally, treatment with KCS inhibitors (K3 herbicides) showed varying inhibitor sensitivities between the duplicated paralogs despite their sequence similarity. Together, this work sheds light on the molecular mechanisms driving substrate diversification in the KCS family and lays the groundwork for tailoring the production of specific VLCFAs.

Long-Chain Acyl-CoA Synthetases Promote Poplar Resistance to Abiotic Stress by Regulating Long-Chain Fatty Acid Biosynthesis

Long-chain acyl-CoA synthetases (LACSs) catalyze fatty acids (FAs) to form fatty acyl-CoA thioesters, which play essential roles in FA and lipid metabolisms and cuticle wax biosynthesis. Although LACSs from Arabidopsis have been intensively studied, the characterization and function of LACSs from poplar are unexplored. Here, 10 poplar PtLACS genes were identified from the poplar genome and distributed to eight chromosomes. A phylogenetic tree indicated that PtLACSs are sorted into six clades. Collinearity analysis and duplication events demonstrated that PtLACSs expand through segmental replication events and experience purifying selective pressure during the evolutionary process. Expression patterns revealed that PtLACSs have divergent expression changes in response to abiotic stress. Interaction proteins and GO analysis could enhance the understanding of putative interactions among protein and gene regulatory networks related to FA and lipid metabolisms. Cluster networks and long-chain FA (LCFA) and very long-chain FA (VLCFA) content analysis revealed the possible regulatory mechanism in response to drought and salt stresses in poplar. The present study provides valuable information for the functional identification of PtLACSs in response to abiotic stress metabolism in poplar.

Wool Wax Extraction From Washing Effluent and Effect on Olea europea Germination and Growth

Effluents from textile industry using wool pose serious environmental nuisances in Tunisia that are mainly due to their pollutant load and the release of unpleasant odors. In order to minimize these hazards and to take advantage of these wastes for the sake of our environment, the present work consists on valuating wool wax from washing effluent on olive (Olea europea), germination and growth. Extraction was made in water at 70°C or hexane using sonication followed by concentration of the extracts in soxhlet apparatus. Results showed that this waste is characterized by its richness in total lipid content with extraction yields of 60.7 and 95.6%, respectively. GC-MS analysis of wax showed its richness on fatty acids. Six saturated fatty acids ranking from 15 to 27 carbon atoms were characterized. Furthermore, diluted wax at a dose of 1.25 mg/g significantly improves germination of olive seeds by germination index calculation, to reach a maximum of 150 ± 17%. In fertigation experiment, the use of the same dose of diluted wax promotes plant length to reach 45.7 ± 2.52 cm. GC-MS analysis after derivatization showed significant enhancement of auxin production in plants treated with 1.25 mg of wax/g of soil compared to control with a concentration of 1.1 ± .1 and .7 ± .2 ng/mg, respectively. This leads us to valuate wool wax as environmental friendly natural product in agricultural and fertigation practice of olive plant.

PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana

Lateral root organogenesis is a key process in the development of a plant's root system and its adaptation to the environment. During lateral root formation, an early phase of cell proliferation first produces a four-cell-layered primordium, and only from this stage onwards is a root meristem-like structure, expressing root stem cell niche marker genes, being established in the developing organ. Previous studies reported that the gene regulatory network controlling lateral root formation is organized into two subnetworks whose mutual inhibition may contribute to organ patterning. PUCHI encodes an AP2/ERF transcription factor expressed early during lateral root primordium development and required for correct lateral root formation. To dissect the molecular events occurring during this early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 mutants and wild types. Transcriptomic and reporter analyses revealed that meristem-related genes were expressed ectopically at early stages of lateral root formation in puchi-1 mutants. We conclude that, consistent with the inhibition of genetic modules contributing to lateral root development, PUCHI represses ectopic establishment of meristematic cell identities at early stages of organ development. These findings shed light on gene network properties that orchestrate correct timing and patterning during lateral root formation.

Regulators regulated: Different layers of control for plasma membrane phosphoinositides in plants

The membranes of plant cells serve diverse physiological roles, which are defined largely by the localized and dynamic recruitment of proteins. Signaling lipids, such as phosphoinositides, can aid protein recruitment to the plasma membrane via specific recognition of their head groups and influence vesicular trafficking, cytoskeletal dynamics and other processes, with ramifications for plant tissue architecture and development. Phosphoinositide abundance is dynamically regulated. Recent advances indicate various levels of control during development or upon environmental triggers, including transcriptional or posttranslational regulation of enzymes balancing biogenesis and degradation, or the nano-organization of membranes into self-organizing physiologically distinct microenvironments. As patterns of interlinked mechanisms emerge, the horizons of what we do not understand become more and more defined.

Protein-protein interactions in fatty acid elongase complexes are important for very-long-chain fatty acid synthesis

Fatty acid elongase (FAE), which catalyzes the synthesis of very-long-chain fatty acids (VLCFAs), is a multiprotein complex; however, little is known about its quaternary structure. In this study, bimolecular fluorescence complementation and/or yeast two-hybrid assays showed that homo-interactions were observed in β-ketoacyl-CoA synthases (KCS2, KCS9, and KCS6), Eceriferum2-like proteins [CER2 and CER2-Like2 (C2L2)], and FAE complex proteins (KCR1, PAS2, ECR, and PAS1), except for CER2-Like1 (C2L1). Hetero-interactions were observed between KCSs (KCS2, KCS9, and KCS6), between CER2-LIKEs (CER2, C2L2, and C2L1), and between FAE complex proteins (KCR1, PAS2, ECR, and PAS1). PAS1 interacts with FAE complex proteins (KCR1, PAS2, and ECR), but not with KCSs (KCS2, KCS9, and KCS6) and CER2-LIKEs (CER2, C2L2, and C2L1). Asp308 and Arg309-Arg311 of KCS9 were essential for the homo-interactions of KCS9 and hetero-interactions between KCS9 and PAS2 or ECR. Asp339 of KCS9 is involved in its homo- and hetero-interactions with ECR. Complementation analysis of the Arabidopsis kcs9 mutant by the expression of amino acid-substituted KCS9 mutant genes showed that Asp308 and Asp339 of KCS9 are involved in the synthesis of C24 VLCFAs from C22. This study suggests that protein-protein interaction in FAE complexes is important for VLCFA synthesis and provides insight into the quaternary structure of FAE complexes for efficient synthesis of VLCFAs.

Synthesis of C20-38 Fatty Acids in Plant Tissues

Very-long-chain fatty acids (VLCFA) are involved in a number of important plant physiological functions. Disorders in the expression of genes involved in the synthesis of VLCFA lead to a number of phenotypic consequences, ranging from growth retardation to the death of embryos. The elongation of VLCFA in the endoplasmic reticulum (ER) is carried out by multiple elongase complexes with different substrate specificities and adapted to the synthesis of a number of products required for a number of metabolic pathways. The information about the enzymes involved in the synthesis of VLCFA with more than 26 atoms of Carbon is rather poor. Recently, genes encoding enzymes involved in the synthesis of both regular-length fatty acids and VLCFA have been discovered and investigated. Polyunsaturated VLCFA in plants are formed mainly by 20:1 elongation into new monounsaturated acids, which are then imported into chloroplasts, where they are further desaturated. The formation of saturated VLCFA and their further transformation into a number of aliphatic compounds included in cuticular waxes and suberin require the coordinated activity of a large number of different enzymes.

Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.

Better together: Protein partnerships for lineage-specific oil accumulation

Plant-derived oils are a major agricultural product that exist in both ubiquitous forms such as common vegetable oils and in specialized forms such as castor oil and coconut oil. These specialized oils are the result of lineage-specific metabolic pathways that create oils rich in unusual fatty acids. Considerable progress has been made toward understanding the enzymes that mediate fatty acid biosynthesis, triacylglycerol assembly, and oil storage. However, efforts to translate this knowledge into renewable bioproducts via engineered oil-producing plants and algae have had limited success. Here, we review recent evidence that protein-protein interactions in each of the three major phases of oil formation appear to have profound effects on specialized oil accumulation. We suggest that furthering our knowledge of the noncatalytic attributes of enzymes and other proteins involved in oil formation will be a critical step toward creating renewable bioproducts derived from high performing, engineered oilseeds.

Extracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls

Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots. Suberin is deposited in most suberizing cells in the form of lamellae just outside of the plasma membrane, below the primary cell wall. How monomeric suberin precursors, thought to be synthesized at the endoplasmic reticulum, are transported outside of the cell, for polymerization into suberin lamellae has remained obscure. Using electron-microscopy, we observed large numbers of extracellular vesiculo-tubular structures (EVs) to accumulate specifically in suberizing cells, in both chemically and cryo-fixed samples. EV presence correlates perfectly with root suberization and we could block suberin deposition and vesicle accumulation by affecting early, as well as late steps in the secretory pathway. Whereas many previous reports have described EVs in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in the formation of a major cell wall polymer.

Suberizing plant cells export suberin monomers outside of the cell to form a hydrophobic barrier. Here the authors propose a role for extracellular vesiculo-tubular structures in the deposition of suberin monomers.

Auxin Transporters-A Biochemical View

From embryogenesis to fruit formation, almost every aspect of plant development and differentiation is controlled by the cellular accumulation or depletion of auxin from cells and tissues. The respective auxin maxima and minima are generated by cell-to-cell auxin transport via transporter proteins. Differential auxin accumulation as a result of such transport processes dynamically regulates auxin distribution during differentiation. In this review, we introduce all auxin transporter (families) identified to date and discuss the knowledge on prominent family members, namely, the PIN-FORMED exporters, ATP-binding cassette B (ABCB)-type transporters, and AUX1/LAX importers. We then concentrate on the biochemical features of these transporters and their regulation by posttranslational modifications and interactors.

Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Plant and fruit surfaces are covered with cuticle wax and provide a protective barrier against biotic and abiotic stresses. Cuticle wax consists of very-long-chain fatty acids (VLCFAs) and their derivatives. β-Ketoacyl-CoA synthase (KCS) is a key enzyme in the synthesis of VLCFAs and provides a precursor for the synthesis of cuticle wax, but the KCS gene family was yet to be reported in the passion fruit (Passiflora edulis). In this study, thirty-two KCS genes were identified in the passion fruit genome and phylogenetically grouped as KCS1-like, FAE1-like, FDH-like, and CER6-like. Furthermore, thirty-one PeKCS genes were positioned on seven chromosomes, while one PeKCS was localized to the unassembled genomic scaffold. The cis-element analysis provides insight into the possible role of PeKCS genes in phytohormones and stress responses. Syntenic analysis revealed that gene duplication played a crucial role in the expansion of the PeKCS gene family and underwent a strong purifying selection. All PeKCS proteins shared similar 3D structures, and a protein-protein interaction network was predicted with known Arabidopsis proteins. There were twenty putative ped-miRNAs which were also predicted that belong to nine families targeting thirteen PeKCS genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation results were highly associated with fatty acid synthase and elongase activity, lipid metabolism, stress responses, and plant-pathogen interaction. The highly enriched transcription factors (TFs) including ERF, MYB, Dof, C2H2, TCP, LBD, NAC, and bHLH were predicted in PeKCS genes. qRT-PCR expression analysis revealed that most PeKCS genes were highly upregulated in leaves including PeKCS2, PeKCS4, PeKCS8, PeKCS13, and PeKCS9 but not in stem and roots tissues under drought stress conditions compared with controls. Notably, most PeKCS genes were upregulated at 9th dpi under Fusarium kyushuense biotic stress condition compared to controls. This study provides a basis for further understanding the functions of KCS genes, improving wax and VLCFA biosynthesis, and improvement of passion fruit resistance.

The features of the fatty acid composition of Pyrus L. total lipids are determined by mountain ecosystem conditions

The composition of fatty acids (FAs) of total lipids of pericarp, seeds, and leaves of Pyrus caucasica Fed. and Pyrus communis L. growing in mountain ecosystems at different altitudes (300, 700 and 1200 m) was studied. It was found that the greatest differences in the relative content of FAs within a species, depending on the altitudes above sea level, were characteristic of the outer tissues of the pericarp (peel) and leaves, which were in direct contact with the external environment. Pericarp parenchyma to a lesser extent, and seeds practically did not differ in FA composition at different heights. At altitudes with increased UV radiation, conjugated octadecadienoates: rumenic acid (9,11-18:2) and 10,12-18:2 were registered in the pericarp and leaf of Purys L., the functions of which in plants were practically not studied. The wild P. caucasica at all growing altitudes was characterized by more very-long-chain FAs (VLCFAs) than the P. communis cultivar. At 700 m, most likely when exposed to fungal infections, the relative number of VLCFAs increased significantly, and new species of individual odd-chaine FAs appeared in their composition in both representatives. It was especially worth noting the appearance in peel and leaf melissic acid (30:0), which was rarely recorded in the plant. A characteristic feature of only P. communis at an altitude of 700 m was the large number of unsaturated individual VLCFAs. Based on the data obtained, a scheme of possible pathways for VLCFA biosynthesis in P. communis were proposed.

Fatty acid export protein BnFAX6 functions in lipid synthesis and axillary bud growth in Brassica napus

Sugar is considered as the primary regulator of plant apical dominance, whereby the outgrowth of axillary buds is inhibited by the shoot tip. However, there are some deficiencies in this theory. Here, we reveal that Fatty Acid Export 6 (BnFAX6) functions in FA transport, and linoleic acid or its derivatives acts as a signaling molecule in regulating apical dominance of Brassica napus. BnFAX6 is responsible for mediating FA export from plastids. Overexpression of BnFAX6 in B. napus heightened the expression of genes involved in glycolysis and lipid biosynthesis, promoting the flow of photosynthetic products to the biosynthesis of FAs (including linoleic acid and its derivatives). Enhancing expression of BnFAX6 increased oil content in seeds and leaves and resulted in semi-dwarf and increased branching phenotypes with more siliques, contributing to increased yield per plant relative to wild-type. Furthermore, decapitation led to the rapid flow of the carbon from photosynthetic products to FA biosynthesis in axillary buds, consistent with the overexpression of BnFAX6 in B. napus. In addition, free FAs, especially linoleic acid, were rapidly transported from leaves to axillary buds. Increasing linoleic acid in axillary buds repressed expression of a key transcriptional regulator responsible for maintaining bud dormancy, resulting in bud outgrowth. Taken together, we uncovered that BnFAX6 mediating FA export from plastids functions in lipid biosynthesis and in axillary bud dormancy release, possibly through enhancing linoleic acid level in axillary buds of B. napus.

Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum)

Cotton seeds are typically covered by lint and fuzz fibres. Natural 'fuzzless' mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome-wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDEL_FZ , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDEL_FZ was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant-repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co-expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very-long-chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.

Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis

Diospyros lotus L. (Date plum) is an important tree species that produces fruit with a high nutritional value. An accurate chromosomal assembly of a species facilitates research on chromosomal evolution and functional gene mapping. In this study, we assembled the first chromosome-level genomes of seeded and seedless D. lotus using Illumina short reads, PacBio long reads, and Hi-C technology. The assembled genomes comprising 15 chromosomes were 617.66 and 647.31 Mb in size, with a scaffold N50 of 40.72 and 42.67 Mb for the seedless and seeded D. lotus, respectively. A BUSCO analysis revealed that the seedless and seeded D. lotus genomes were 91.53% and 91.60% complete, respectively. Additionally, 20,689 (95.4%) and 22,844 (98.5%) protein-coding genes in the seedless and seeded D. lotus genomes were annotated, respectively. Comparisons of the chromosomes between genomes revealed inversions and translocations on chromosome 8 and inversions on chromosome 11. We identified 490 and 424 gene families that expanded in the seedless and seeded D. lotus, respectively. The enriched pathways among these gene families included the estrogen signaling pathway, the MAPK signaling pathway, and biosynthetic pathways for flavonoids, monoterpenoids, and glucosinolates. Moreover, we constructed the first Diospyros genome database (http://www.persimmongenome.cn). On the basis of our data, we developed the first high-quality annotated D. lotus reference genomes, which will be useful for genomic studies on persimmon and for clarifying the molecular mechanisms underlying important traits. Comparisons between the seeded and seedless D. lotus genomes may also elucidate the molecular basis of seedlessness.

Biosynthesis and Functions of Very-Long-Chain Fatty Acids in the Responses of Plants to Abiotic and Biotic Stresses

Very-long-chain fatty acids (i.e., fatty acids with more than 18 carbon atoms; VLCFA) are important molecules that play crucial physiological and structural roles in plants. VLCFA are specifically present in several membrane lipids and essential for membrane homeostasis. Their specific accumulation in the sphingolipids of the plasma membrane outer leaflet is of primordial importance for its correct functioning in intercellular communication. VLCFA are found in phospholipids, notably in phosphatidylserine and phosphatidylethanolamine, where they could play a role in membrane domain organization and interleaflet coupling. In epidermal cells, VLCFA are precursors of the cuticular waxes of the plant cuticle, which are of primary importance for many interactions of the plant with its surrounding environment. VLCFA are also major components of the root suberin barrier, which has been shown to be fundamental for nutrient homeostasis and plant adaptation to adverse conditions. Finally, some plants store VLCFA in the triacylglycerols of their seeds so that they later play a pivotal role in seed germination. In this review, taking advantage of the many studies conducted using Arabidopsis thaliana as a model, we present our current knowledge on the biosynthesis and regulation of VLCFA in plants, and on the various functions that VLCFA and their derivatives play in the interactions of plants with their abiotic and biotic environment.

Ceramides mediate positional signals in Arabidopsis thaliana protoderm differentiation

The differentiation of distinct cell types in appropriate patterns is a fundamental process in the development of multicellular organisms. In Arabidopsis thaliana, protoderm/epidermis differentiates as a single cell layer at the outermost position. However, little is known about the molecular nature of the positional signals that achieve correct epidermal cell differentiation. Here, we propose that very-long-chain fatty acid-containing ceramides (VLCFA-Cers) mediate positional signals by stimulating the function of ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), a master regulator of protoderm/epidermis differentiation, during lateral root development. We show that VLCFA-Cers, which are synthesized predominantly in the outermost cells, bind to the lipid-binding domain of ATML1. Importantly, this cell type-specific protein-lipid association alters the activity of ATML1 protein and consequently restricts its expression to the protoderm/epidermis through a transcriptional feedback loop. Furthermore, establishment of a compartment, enriched with VLCFA-containing sphingolipids, at the outer lateral membrane facing the external environment may function as a determinant of protodermal cell fate. Taken together, our results indicate that VLCFA-Cers play a pivotal role in directing protoderm/epidermis differentiation by mediating positional signals to ATML1.This article has an associated 'The people behind the papers' interview.

The 3-ketoacyl-CoA synthase WFL is involved in lateral organ development and cuticular wax synthesis in Medicago truncatula

A 3-ketoacyl-CoA synthase involved in biosynthesis of very long chain fatty acids and cuticular wax plays a vital role in aerial organ development in M. truncatula. Cuticular wax is composed of very long chain fatty acids and their derivatives. Defects in cuticular wax often result in organ fusion, but little is known about the role of cuticular wax in compound leaf and flower development in Medicago truncatula. In this study, through an extensive screen of a Tnt1 retrotransposon insertion population in M. truncatula, we identified four mutant lines, named wrinkled flower and leaf (wfl) for their phenotype. The phenotype of the wfl mutants is caused by a Tnt1 insertion in Medtr3g105550, encoding 3-ketoacyl-CoA synthase (KCS), which functions as a rate-limiting enzyme in very long chain fatty acid elongation. Reverse transcription-quantitative PCR showed that WFL was broadly expressed in aerial organs of the wild type, such as leaves, floral organs, and the shoot apical meristem, but was expressed at lower levels in roots. In situ hybridization showed a similar expression pattern, mainly detecting the WFL transcript in epidermal cells of the shoot apical meristem, leaf primordia, and floral organs. The wfl mutant leaves showed sparser epicuticular wax crystals on the surface and increased water permeability compared with wild type. Further analysis showed that in wfl leaves, the percentage of C20:0, C22:0, and C24:0 fatty acids was significantly increased, the amount of cuticular wax was markedly reduced, and wax constituents were altered compared to the wild type. The reduced formation of cuticular wax and wax composition changes on the leaf surface might lead to the developmental defects observed in the wfl mutants. These findings suggest that WFL plays a key role in cuticular wax formation and in the late stage of leaf and flower development in M. truncatula.

High level accumulation of EPA and DHA in field-grown transgenic Camelina - a multi-territory evaluation of TAG accumulation and heterogeneity

The transgene-directed accumulation of non-native omega-3 long chain polyunsaturated fatty acids in the seed oil of Camelina sativa (Camelina) was evaluated in the field, in distinct geographical and regulatory locations. A construct, DHA2015.1, containing an optimal combination of biosynthetic genes, was selected for experimental field release in the UK, USA and Canada, and the accumulation of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) determined. The occurrence of these fatty acids in different triacylglycerol species was monitored and found to follow a broad trend irrespective of the agricultural environment. This is a clear demonstration of the stability and robust nature of the transgenic trait for omega-3 long chain polyunsaturated fatty acids in Camelina. Examination of non-seed tissues for the unintended accumulation of EPA and DHA failed to identify their presence in leaf, stem, flower, anther or capsule shell material, confirming the seed-specific accumulation of these novel fatty acids. Collectively, these data confirm the promise of GM plant-based sources of so-called omega-3 fish oils as a sustainable replacement for oceanically derived oils.

Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi

Many pathogenic fungi depend on the development of specialized infection structures called appressoria to invade their hosts and cause disease. Impairing the function of fungal infection structures therefore provides a potential means by which diseases could be prevented. In spite of this extraordinary potential, however, relatively few anti-penetrant drugs have been developed to control fungal diseases, of either plants or animals. In the present study, we report the identification of compounds that act specifically to prevent fungal infection. We found that the organization of septin GTPases, which are essential for appressorium-mediated infection in the rice blast fungus Magnaporthe oryzae, requires very-long-chain fatty acids (VLCFAs), which act as mediators of septin organization at membrane interfaces. VLCFAs promote septin recruitment to curved plasma membranes and depletion of VLCFAs prevents septin assembly and host penetration by M. oryzae. We observed that VLCFA biosynthesis inhibitors not only prevent rice blast disease, but also show effective, broad-spectrum fungicidal activity against a wide range of fungal pathogens of maize, wheat and locusts, without affecting their respective hosts. Our findings reveal a mechanism underlying septin-mediated infection structure formation in fungi and provide a class of fungicides to control diverse diseases of plants and animals.

Metabolic Cellular Communications: Feedback Mechanisms between Membrane Lipid Homeostasis and Plant Development

Membrane lipids are often viewed as passive building blocks of the endomembrane system. However, mounting evidence suggests that sphingolipids, sterols, and phospholipids are specifically targeted by developmental pathways, notably hormones, in a cell- or tissue-specific manner to regulate plant growth and development. Targeted modifications of lipid homeostasis may act as a way to execute a defined developmental program, for example, by regulating other signaling pathways or participating in cell differentiation. Furthermore, these regulations often feed back on the very signaling pathway that initiates the lipid metabolic changes. Here, we review several recent examples highlighting the intricate feedbacks between membrane lipid homeostasis and plant development. In particular, these examples illustrate how all aspects of membrane lipid metabolic pathways are targeted by these feedback regulations. We propose that the time has come to consider membrane lipids and lipid metabolism as an integral part of the developmental program needed to build a plant.

Auxin treatment of grapevine (Vitis vinifera L.) berries delays ripening onset by inhibiting cell expansion

Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.

AKR2A participates in the regulation of cotton fibre development by modulating biosynthesis of very-long-chain fatty acids

The biosynthesis of very-long-chain fatty acids (VLCFAs) and their transport are required for fibre development. However, whether other regulatory factors are involved in this process is unknown. We report here that overexpression of an Arabidopsis gene ankyrin repeat-containing protein 2A (AKR2A) in cotton promotes fibre elongation. RNA-Seq analysis was employed to elucidate the mechanisms of AKR2A in regulating cotton fibre development. The VLCFA content and the ratio of VLCFAs to short-chain fatty acids increased in AKR2A transgenic lines. In addition, AKR2A promotes fibre elongation by regulating ethylene and synergizing with the accumulation of auxin and hydrogen peroxide. Analysis of RNA-Seq data indicates that AKR2A up-regulates transcript levels of genes involved in VLCFAs' biosynthesis, ethylene biosynthesis, auxin and hydrogen peroxide signalling, cell wall and cytoskeletal organization. Furthermore, AKR2A interacted with KCS1 in Arabidopsis both in vitro and in vivo. Moreover, the VLCFA content and the ratio of VLCFAs to short-chain fatty acids increased significantly in seeds of AKR2A-overexpressing lines and AKR2A/KCS1 co-overexpressing lines, while AKR2A mutants are the opposite trend. Our results uncover a novel cotton fibre growth mechanism by which the critical regulator AKR2A promotes fibre development via activating hormone signalling cascade by mediating VLCFA biosynthesis. This study provides a potential candidate gene for improving fibre yield and quality through genetic engineering.

GFP Scaffold-Based Engineering for the Production of Unbranched Very Long Chain Fatty Acids in Escherichia coli With Oleic Acid and Cerulenin Supplementation

Currently, very long chain fatty acids (VLCFAs) for oleochemical, pharmaceutical, cosmetic, or food applications are extracted from plant or marine organism resources, which is associated with a negative environmental impact. Therefore, there is an industrial demand to develop sustainable, microbial resources. Due to its ease of genetic modification and well-characterized metabolism, Escherichia coli has established itself as a model organism to study and tailor microbial fatty acid biosynthesis using a concerted genetic engineering approach. In this study, we systematically implemented a plant-derived (Arabidopsis thaliana) enzymatic cascade in Escherichia coli to enable unbranched VLCFA biosynthesis. The four Arabidopsis thaliana membrane-bound VLCFA enzymes were expressed using a synthetic expression cassette. To facilitate enzyme solubilization and interaction of the synthetic VLCFA synthase complex, we applied a self-assembly GFP scaffold. In order to initiate VLCFA biosynthesis, external oleic acid and cerulenin were supplemented to cultures. In this context, we detected the generation of arachidic (20:0), cis-11-eicosenoic (20:1) and cis-13-eicosenoic acid (20:1).

Molecular Dialog Between Parasitic Plants and Their Hosts

Parasitic plants steal sugars, water, and other nutrients from host plants through a haustorial connection. Several species of parasitic plants such as witchweeds (Striga spp.) and broomrapes (Orobanche and Phelipanche spp.) are major biotic constraints to agricultural production. Parasitic plants are understudied compared with other major classes of plant pathogens, but the recent availability of genomic and transcriptomic data has accelerated the rate of discovery of the molecular mechanisms underpinning plant parasitism. Here, we review the current body of knowledge of how parasitic plants sense host plants, germinate, form parasitic haustorial connections, and suppress host plant immune responses. Additionally, we assess whether parasitic plants fit within the current paradigms used to understand the molecular mechanisms of microbial plant-pathogen interactions. Finally, we discuss challenges facing parasitic plant research and propose the most urgent questions that need to be answered to advance our understanding of plant parasitism.