Isolation and characterization of mutants defective in seed coat mucilage secretory cell development in Arabidopsis

Imaging plant cell walls using fluorescent stains: The beauty is in the details

Plants continuously face various environmental stressors throughout their lifetime. To be able to grow and adapt in different environments, they developed specialized tissues that allowed them to maintain a protected yet interconnected body. These tissues undergo specific primary and secondary cell wall modifications that are essential to ensure normal plant growth, adaptation and successful land colonization. The composition of cell walls can vary among different plant species, organs and tissues. The ability to remodel their cell walls is fundamental for plants to be able to cope with multiple biotic and abiotic stressors. A better understanding of the changes taking place in plant cell walls may help identify and develop new strategies as well as tools to enhance plants' survival under environmental stresses or prevent pathogen attack. Since the invention of microscopy, numerous imaging techniques have been developed to determine the composition and dynamics of plant cell walls during normal growth and in response to environmental stimuli. In this review, we discuss the main advances in imaging plant cell walls, with a particular focus on fluorescent stains for different cell wall components and their compatibility with tissue clearing techniques. Lay Description: Plants are continuously subjected to various environmental stresses during their lifespan. They evolved specialized tissues that thrive in different environments, enabling them to maintain a protected yet interconnected body. Such tissues undergo distinct primary and secondary cell wall alterations essential to normal plant growth, their adaptability and successful land colonization. Cell wall composition may differ among various plant species, organs and even tissues. To deal with various biotic and abiotic stresses, plants must have the capacity to remodel their cell walls. Gaining insight into changes that take place in plant cell walls will help identify and create novel tools and strategies to improve plants' ability to withstand environmental challenges. Multiple imaging techniques have been developed since the introduction of microscopy to analyse the composition and dynamics of plant cell walls during growth and in response to environmental changes. Advancements in plant tissue cleaning procedures and their compatibility with cell wall stains have significantly enhanced our ability to perform high-resolution cell wall imaging. At the same time, several factors influence the effectiveness of cleaning and staining plant specimens, as well as the time necessary for the process, including the specimen's size, thickness, tissue complexity and the presence of autofluorescence. In this review, we will discuss the major advances in imaging plant cell walls, with a particular emphasis on fluorescent stains for diverse cell wall components and their compatibility with tissue clearing techniques. We hope that this review will assist readers in selecting the most appropriate stain or combination of stains to highlight specific cell wall components of interest.

Research advances on the hard seededness trait of soybean and the underlying regulatory mechanisms

Soybean is one of the world's most economically significant crops and is widely utilized as an essential source of vegetable protein and edible oil. Cultivated soybean is domesticated from its annual counterpart, wild soybean, which is considered valuable germplasm for soybean breeding. However, wild soybean accessions generally produce seeds with impermeable coats, a trait known as hard seededness (HS), which is beneficial for long-term seed survival but is undesirable for the uniform water absorption and germination of seeds, thus limiting the utilization of wild soybeans in breeding. In addition, moderate HS can isolate the embryo from the surrounding environment and is thus beneficial for long-term seed storage and germplasm preservation. The HS trait is primarily associated with the structure and chemical composition of the seed coat. Moreover, its development is also influenced by various environmental conditions, such as water and temperature. Genetic analysis has revealed that HS of soybean is a complex quantitative trait controlled by multiple genes or minor quantitative trait loci (QTL), with many QTLs and several causal genes currently identified. Investigating the physiological and molecular mechanisms underlying this trait is crucial for soybean breeding, production, and food processing. For this article, the literature was reviewed and condensed to create a well-rounded picture of the current understanding of internal and external factors, QTLs, causal genes, and the regulatory mechanisms related to the HS of soybean, with the aim of providing reference for future research and utilization of this trait.

Embryo sac cellularization defects lead to supernumerary egg cells and twin embryos in Arabidopsis thaliana

Arabidopsis lines with loss-of-function mutation in Embryo sac-specific Pectin MethylEsterase Inhibitor (Atepmei) gene showed seed sterility with embryo sac cellularization defects. Examination of tissue-cleared mature ovules revealed irregularly positioned nuclei/embryos within the embryo sacs. Egg cell-specific marker (DD45) expression analysis confirmed the presence of multiple egg cells in the mutant embryo sacs. These supernumerary egg cells were functional as evident from the production of twin embryos when supernumerary sperm cells were provided. The results of ruthenium red and tannic acid-ferric chloride staining of developing Atepmei mutant ovules showed that cell wall formation and maintenance were altered around embryo sac nuclei, which also coincided with change in the gamete specification. This report implicates the role of cell walls in gamete cell fate determination by altering cell-cell communication. Our analysis of the twin-embryo phenotype of epmei mutants also sheds light on the boundary conditions for double fertilization in plant reproduction.

BrTTG1 regulates seed coat proanthocyanidin formation through a direct interaction with structural gene promoters of flavonoid pathway and glutathione S-transferases in Brassica rapa L

Introduction

Seed coat color is a significant agronomic trait in horticultural crops such as Brassica rapa which is characterized by brown or yellow seed coat coloration. Previous Brassica rapa studies have shown that BrTTG1 is responsible for seed coat proanthocyanidin formation, which is dependent on the MYB-bHLH-WD40 complex, whereas some studies have reported that TRANSPARENT TESTA GLABRA 1 (TTG1) directly interacts with the structural gene promoters of the flavonoid pathway.

Methods

Herein, the brown-seeded inbred B147 and ttg1 yellow-seeded inbred B80 mutants were used as plant materials for gene expression level analysis, gene promoter clone and transient overexpression.

Results

The analysis identified eleven structural genes involved in the flavonoid biosynthesis pathway, which are potentially responsible for BrTTG1- dependent seed coat proanthocyanidin formation. The promoters of these genes were cloned and cis-acting elements were identified. Yeast one-hybrid and dual-luciferase assays confirmed that BrTTG1 directly and independently interacted with proCHS-Bra008792, proDFR-Bra027457, proTT12-Bra003361, proTT19-Bra008570, proTT19-Bra023602 and proAHA10-Bra016610. A TTG1-binding motif (RTWWGTRGM) was also identified. Overexpression of TTG1 in the yellow-seed B. rapa inbred induced proanthocyanidin accumulation by increasing the expression levels of related genes.

Discussion

Our study unveiled, for the first time, the direct interaction between TTG1 and the promoters of the flavonoid biosynthesis pathway structural genes and glutathione S-transferases in Brassica rapa. Additionally, we have identified a novel TTG1-binding motif, providing a basis for further exploration into the function of TTG1 and the accumulation of proanthocyanidins in seed coats.

The APETALA2-MYBL2 module represses proanthocyanidin biosynthesis by affecting formation of the MBW complex in seeds of Arabidopsis thaliana

Proanthocyanidins (PAs) are the second most abundant plant phenolic natural products. PA biosynthesis is regulated by the well-documented MYB/bHLH/WD40 (MBW) complex, but how this complex itself is regulated remains ill defined. Here, in situ hybridization and β-glucuronidase staining show that APETALA2 (AP2), a well-defined regulator of flower and seed development, is strongly expressed in the seed coat endothelium, where PAs accumulate. AP2 negatively regulates PA content and expression levels of key PA pathway genes. AP2 activates MYBL2 transcription and interacts with MYBL2, a key suppressor of the PA pathway. AP2 exerts its function by directly binding to the AT-rich motifs near the promoter region of MYBL2. Molecular and biochemical analyses revealed that AP2 forms AP2-MYBL2-TT8/EGL3 complexes, disrupting the MBW complex and thereby repressing expression of ANR, TT12, TT19, and AHA10. Genetic analyses revealed that AP2 functions upstream of MYBL2, TT2, and TT8 in PA regulation. Our work reveals a new role of AP2 as a key regulator of PA biosynthesis in Arabidopsis. Overall, this study sheds new light on the comprehensive regulation network of PA biosynthesis as well as the dual regulatory roles of AP2 in seed development and accumulation of major secondary metabolites in Arabidopsis.

Genome wide association study of Arabidopsis seed mucilage layers at a regional scale

The myxospermous species Arabidopsis thaliana extrudes a polysaccharidic mucilage from the seed coat epidermis during imbibition. The whole seed mucilage can be divided into a seed-adherent layer and a fully soluble layer, both layers presenting natural genetic variations. The adherent mucilage is variable in size and composition, while the soluble mucilage is variable in composition and physical properties. Studies reporting both the genetic architecture and the putative selective agents acting on this natural genetic variation are scarce. In this study, we set up a Genome Wide Association study (GWAS) based on 424 natural accessions collected from 166 natural populations of A. thaliana located south-west of France and previously characterized for a very important number of abiotic and biotic factors. We identified an extensive genetic variation for both mucilage layers. The adherent mucilage was mainly related to precipitation and temperature whereas the non-adherent mucilage was unrelated to any environmental factors. By combining a hierarchical Bayesian model with a local score approach, we identified 55 and 28 candidate genes, corresponding to 26 and 10 QTLs for the adherent and non-adherent mucilages, respectively. Putative or characterized function and expression data available in the literature were used to filter the candidate genes. Only one gene among our set of candidate genes was already described as a seed mucilage actor, leaving a large set of new candidates putatively implicated inseed mucilage synthesis or release. The present study lay out foundation to understand the influence of regional ecological factors acting on seed mucilage in A. thaliana.

Disruption of the Arabidopsis Acyl-Activating Enzyme 3 Impairs Seed Coat Mucilage Accumulation and Seed Germination

The Acyl-activating enzyme (AAE) 3 gene encodes an oxalyl-CoA synthetase that catalyzes the conversion of oxalate to oxalyl-CoA as the first step in the CoA-dependent pathway of oxalate catabolism. Although the role of this enzyme in oxalate catabolism has been established, its biological roles in plant growth and development are less understood. As a step toward gaining a better understanding of these biological roles, we report here a characterization of the Arabidopsis thaliana aae3 (Ataae3) seed mucilage phenotype. Ruthidium red (RR) staining of Ataae3 and wild type (WT) seeds suggested that the observed reduction in Ataae3 germination may be attributable, at least in part, to a decrease in seed mucilage accumulation. Quantitative RT-PCR analysis revealed that the expression of selected mucilage regulatory transcription factors, as well as of biosynthetic and extrusion genes, was significantly down-regulated in the Ataae3 seeds. Mucilage accumulation in seeds from an engineered oxalate-accumulating Arabidopsis and Atoxc mutant, blocked in the second step of the CoA-dependent pathway of oxalate catabolism, were found to be similar to WT. These findings suggest that elevated tissue oxalate concentrations and loss of the oxalate catabolism pathway downstream of AAE3 were not responsible for the reduced Ataae3 seed germination and mucilage phenotypes. Overall, our findings unveil the presence of regulatory interplay between AAE3 and transcriptional control of mucilage gene expression.

Fruit development and ripening orchestrating the biosynthesis and regulation of Lycium barbarum polysaccharides in goji berry

Lycium barbarum polysaccharides (LBPs) are the primary bioactive components in fruits of L. barbarum, commonly known as goji berry. Despite significant progress in understanding the chemical structures and health benefits of LBPs, the biosynthesis and regulation of LBPs in goji berry remains largely unknown. In this study, physiological indicators, including LBPs, were monitored in goji berry during fruit development and ripening (FDR), suggesting that pectin might be the major component of LBPs with increased content reaching 235.8 mg/g DW. Proteomic and transcriptomic analysis show that 6410 differentially expressed genes (DEGs) and 2052 differentially expressed proteins (DEPs) were identified with overrepresentation of flavonoids and polysaccharides-related gene ontology (GO) terms and KEGG pathways. Weighted gene co-expression network analysis (WGCNA) showed that LBPs coexpress with genes involved in pectin biosynthesis (LbGALS3, LbGATL5, LbQUA1, LbGAUT1/4/7, LbRGGAT1, LbRRT1/7, and LbRHM2), modification (LbSBT1.7), and regulation (LbAP2, LbGL2 LbTLP2, LbERF4, and LbTTG2), as well as with novel transcription factors (LbSPL9 and LbRIN homologs) and glycosyltransferases. Transgenic hairy roots overexpressing LbRIN validated that LbRIN modulate the expression of WGCNA-predicted regulators, including LbERF4, LbTTG2, and LbSPL9. These findings suggest that the biosynthesis and regulation of LBPs is conserved partially to those in Arabidopsis pectin. Taken together, this study provides valuable insights into the biosynthesis and regulation of LBPs, which can facilitate future studies on synthetic biology applications and genetic improvement of LBPs.

HD-Zip IV transcription factors: Drivers of epidermal cell fate integrate metabolic signals

The leaf epidermis comprises the outermost layer of cells that protect plants against environmental stresses such as drought, ultraviolet radiation, and pathogen attack. Research over the past decades highlights the role of class IV homeodomain leucine-zipper (HD-Zip IV) transcription factors (TFs) in driving differentiation of various epidermal cell types, such as trichomes, guard cells, and pavement cells. Evolutionary origins of this family in the charophycean green algae and HD-Zip-specific gene expression in the maternal genome provide clues to unlocking their secrets which include ties to cell cycle regulation. A distinguishing feature of these TFs is the presence of a lipid binding pocket that integrates metabolic information with gene expression. Identities of metabolic partners are beginning to emerge, uncovering feedback loops to maintain epidermal cell specification. Discoveries of associated molecular mechanisms are revealing fascinating links to phospholipid and sphingolipid metabolism and mechanical signaling.

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.

Kaempferol-3-rhamnoside overaccumulation in flavonoid 3'-hydroxylase tt7 mutants compromises seed coat outer integument differentiation and seed longevity

Seeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat protects the embryo from the external environment, and its composition is critical for seed longevity. Flavonols accumulate in the outer integument. The link between flavonol composition and outer integument development has not been explored. Genetic, molecular and ultrastructural assays on loss-of-function mutants of the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition on seed coat development and seed longevity. Controlled deterioration assays indicate that loss of function of the flavonoid 3' hydroxylase gene TT7 dramatically affects seed longevity and seed coat development. Outer integument differentiation is compromised from 9 d after pollination in tt7 developing seeds, resulting in a defective suberin layer and incomplete degradation of seed coat starch. These distinctive phenotypes are not shared by other mutants showing abnormal flavonoid composition. Genetic analysis indicates that overaccumulation of kaempferol-3-rhamnoside is mainly responsible for the observed phenotypes. Expression profiling suggests that multiple cellular processes are altered in the tt7 mutant. Overaccumulation of kaempferol-3-rhamnoside in the seed coat compromises normal seed coat development. This observation positions TRANSPARENT TESTA 7 and the UGT78D1 glycosyltransferase, catalysing flavonol 3-O-rhamnosylation, as essential players in the modulation of seed longevity.

Contrasting Cd accumulation of Arabidopsis halleri populations: a role for (1→4)-β-galactan in pectin

Cadmium (Cd) accumulation is highly variable among Arabidopsis halleri populations. To identify cell wall (CW) components that contribute to the contrasting Cd accumulation between PL22-H (Cd-hyperaccumulator) and I16-E (Cd-excluder), Cd absorption capacity of CW polysaccharides, CW mono- and poly- saccharides contents and CW glycan profiles were compared between these two populations. PL22-H pectin contained 3-fold higher Cd concentration than I16-E pectin in roots, and (1→4)-β-galactan pectic epitope showed the biggest difference between PL22-H and I16-E. CW-related differentially expressed genes (DEGs) between PL22-H and I16-E were identified and corresponding A. thaliana mutants were phenotyped for Cd tolerance and accumulation. A higher Cd translocation was observed in GALACTAN SYNTHASE1 A. thaliana knockout and overexpressor mutants, which both showed a lengthening of the RG-I sidechains after Cd treatment, contrary to the wild-type. Overall, our results support an indirect role for (1→4)-β-galactan in Cd translocation, possibly by a joint effect of regulating the length of RG-I sidechains, the pectin structure and interactions between polysaccharides in the CW. The characterization of other CW-related DEGs between I16-E and PL22-H selected allowed to identify a possible role in Zn translocation for BIIDXI and LEUNIG-HOMOLOG genes, which are both involved in pectin modification.

Regulation of seed coat mucilage production and modification in Arabidopsis

The Arabidopsis seed coat mucilage is a polysaccharide-rich matrix synthesized by the seed coat epidermal cells. It is a specialized cell wall mainly composed of three types of polysaccharides (i. e. pectin, hemicellulose, and cellulose), and represents as an ideal model system for plant cell wall research. A large number of genes responsible for the synthesis and modification of cell wall polysaccharides have been identified using this model system. Moreover, a subset of regulators controlling mucilage production and modification have been characterized, and the underlying transcriptional regulatory mechanisms have been elucidated. This substantially contributes to the understanding of the molecular mechanisms underlying mucilage synthesis and modification. In this review, we concisely summarize the various genes and regulators involved in seed coat cell differentiation, mucilage biosynthesis and modification, and secondary cell wall formation. In particular, we put emphasis on the latest knowledge gained regarding the transcriptional regulation of mucilage production, which is composed of a hierarchal cascade with three-layer transcriptional regulators. Collectively, we propose an updated schematic framework of the genetic regulatory network controlling mucilage production and modification in the Arabidopsis mucilage secretory cells.

Novel constituents of Salvia hispanica L. (chia) nutlet mucilage and the improved in vitro fermentation of nutlets when ground

Upon wetting, chia (Salvia hispanica L.) nutlets produce a gel-like capsule of polysaccharides called mucilage that comprises a significant part of their dietary fibre content. Seed/nutlet mucilage is often used as a texture modifying hydrocolloid and bulking dietary fibre due to its water-binding ability, though the utility of mucilage from different sources is highly structure-function dependent. The composition and structure of chia nutlet mucilage is poorly defined, and a better understanding will aid in exploiting its dietary fibre functionality, particularly if, and how, it is utilised by gut microbiota. In this study, microscopy, chromatography, mass spectrometry and glycome profiling techniques showed that chia nutlet mucilage is highly complex, layered, and contains several polymer types. The mucilage comprises a novel xyloamylose containing both β-linked-xylose and α-linked-glucose, a near-linear xylan that may be sparsely substituted, a modified cellulose domain, and abundant alcohol-soluble oligosaccharides. To assess the dietary fibre functionality of chia nutlet mucilage, an in vitro cumulative gas production technique was used to determine the fermentability of different chia nutlet preparations. The complex nature of chia nutlet mucilage led to poor fermentation where the oligosaccharides appeared to be the only fermentable substrate present in the mucilage. Of note, ground chia nutlets were better fermented than intact whole nutlets, as judged by short chain fatty acid production. Therefore, it is suggested that the benefits of eating chia as a "superfood", could be notably enhanced if the nutlets are ground rather than being consumed whole, improving the bioaccessibility of key nutrients including dietary fibre.

EYFP fusions to HD-Zip IV transcription factors enhance their stability and lead to phenotypic changes in Arabidopsis

Green fluorescent protein (GFP) and its derivatives are extensively used for labeling cells, monitoring gene expression and/or tracking the localization or interactions of proteins. Previous reports of detrimental effects of fluorescent protein (FP) expression include cytotoxicity and interference with fusion protein function or localization. Only a few studies have documented the fluorescent tag-specific effects in plants. Here, we show that placing an enhanced yellow FP (EYFP) tag on the amino-terminus of GLABRA2 (GL2) and PROTODERMAL FACTOR2 (PDF2), two developmentally important HD-Zip IV transcription factors from Arabidopsis, enhances their protein stability. Additionally, expression of EYFP:GL2 not only rescued the gl2 null mutant but also resulted in the abnormal development of abaxially curled leaves associated with EYFP-tag induced GL2 overexpression. Our study raises concerns on the use of FPs regarding their effects on the native properties of target proteins as well as biological consequences of fusion protein expression on morphology.

The START domain mediates Arabidopsis GLABRA2 dimerization and turnover independently of homeodomain DNA binding

Class IV homeodomain leucine-zipper transcription factors (HD-Zip IV TFs) are key regulators of epidermal differentiation that are characterized by a DNA-binding HD in conjunction with a lipid-binding domain termed steroidogenic acute regulatory-related lipid transfer (START). Previous work established that the START domain of GLABRA2 (GL2), a HD-Zip IV member from Arabidopsis (Arabidopsis thaliana), is required for TF activity. Here, we addressed the functions and possible interactions of START and the HD in DNA binding, dimerization, and protein turnover. Deletion analysis of the HD and missense mutations of a conserved lysine (K146) resulted in phenotypic defects in leaf trichomes, root hairs, and seed mucilage, similar to those observed for START domain mutants, despite nuclear localization of the respective proteins. In vitro and in vivo experiments demonstrated that while HD mutations impair binding to target DNA, the START domain is dispensable for DNA binding. Vice versa, protein interaction assays revealed impaired GL2 dimerization for multiple alleles of START mutants, but not HD mutants. Using in vivo cycloheximide chase experiments, we provided evidence for the role of START, but not HD, in maintaining protein stability. This work advances our mechanistic understanding of HD-Zip TFs as multidomain regulators of epidermal development in plants.

The Genetic Control of SEEDSTICK and LEUNIG-HOMOLOG in Seed and Fruit Development: New Insights into Cell Wall Control

Although much is known about seed and fruit development at the molecular level, many gaps remain in our understanding of how cell wall modifications can impact developmental processes in plants, as well as how biomechanical alterations influence seed and fruit growth. Mutants of Arabidopsis thaliana constitute an excellent tool to study the function of gene families devoted to cell wall biogenesis. We have characterized a collection of lines carrying mutations in representative cell wall-related genes for seed and fruit size developmental defects, as well as altered germination rates. We have linked these studies to cell wall composition and structure. Interestingly, we have found that disruption of genes involved in pectin maturation and hemicellulose deposition strongly influence germination dynamics. Finally, we focused on two transcriptional regulators, SEEDSTICK (STK) and LEUNIG-HOMOLOG (LUH), which positively regulate seed growth. Herein, we demonstrate that these factors regulate specific aspects of cell wall properties such as pectin distribution. We propose a model wherein changes in seed coat structure due to alterations in the xyloglucan-cellulose matrix deposition and pectin maturation are critical for organ growth and germination. The results demonstrate the importance of cell wall properties and remodeling of polysaccharides as major factors responsible for seed development.

Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives

Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.

Seed Transmission of Pathogens: Non-Canonical Immune Response in Arabidopsis Germinating Seeds Compared to Early Seedlings against the Necrotrophic Fungus Alternaria brassicicola

The transmission of seed-borne pathogens by the germinating seed is responsible for major crop diseases. The immune responses of the seed facing biotic invaders are poorly documented so far. The Arabidopsis thaliana/Alternaria brassicicola patho-system was used to describe at the transcription level the responses of germinating seeds and young seedling stages to infection by the necrotrophic fungus. RNA-seq analyses of healthy versus inoculated seeds at 3 days after sowing (DAS), stage of radicle emergence, and at 6 and 10 DAS, two stages of seedling establishment, identified thousands of differentially expressed genes by Alternaria infection. Response to hypoxia, ethylene and indole pathways were found to be induced by Alternaria in the germinating seeds. However, surprisingly, the defense responses, namely the salicylic acid (SA) pathway, the response to reactive oxygen species (ROS), the endoplasmic reticulum-associated protein degradation (ERAD) and programmed cell death, were found to be strongly induced only during the latter post-germination stages. We propose that this non-canonical immune response in early germinating seeds compared to early seedling establishment was potentially due to the seed-to-seedling transition phase. Phenotypic analyses of about 14 mutants altered in the main defense pathways illustrated these specific defense responses. The unexpected germination deficiency and insensitivity to Alternaria in the glucosinolate deficient mutants allow hypothesis of a trade-off between seed germination, necrosis induction and Alternaria transmission to the seedling. The imbalance of the SA and jasmonic acid (JA) pathways to the detriment of the JA also illustrated a non-canonical immune response at the first stages of the seedling.

Rhamnogalacturonan-I forms mucilage: behind its simplicity, a cutting-edge organization

Zhang Y, Yin Q, Qin W, Gao H, Du J, Chen J, Li H, Zhou G, Wu H, Wu A-M. 2022. The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis. Journal of Experimental Botany 73, 3477–3495.

The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis

The production of Arabidopsis seed mucilage involves complex polysaccharide biosynthetic pathways and developmental processes in seed epidermal cells. Although the polysaccharide components of Arabidopsis seed mucilage have been identified, their regulatory mechanism requires further investigation. Here, we show that Class II KNOX gene family members KNAT3 and KNAT7 play an essential role in regulating mucilage production in the early developmental stages of Arabidopsis seeds. Double mutant knat3knat7 resulted in defective seed mucilage production and columellae formation, whereas knat3 showed a normal phenotype compared with wild type, and the mucilage thickness in knat7 was slightly disturbed. Rhamnogalacturonan I (RG-I) and its biosynthetic substrates galacturonic acid and rhamnose were reduced in both the adherent and soluble mucilage of knat3knat7. Comparative transcriptome analysis on whole seeds suggested that polysaccharide, glucosinolate and anthocyanin biosynthetic pathways were specifically repressed in knat3knat7. Transient co-expression of KNAT3 and KNAT7 with promoter regions of candidate genes in Arabidopsis protoplasts revealed that both KNAT3 and KNAT7 act as positive regulators of the RG-I biosynthetic gene MUCILAGE-MODIFIED 4 (MUM4, AT1G53500). Collectively, our results demonstrate that KNAT3 and KNAT7 are multifunctional transcription factors in secondary cell wall development and redundantly modulate mucilage biosynthesis in Arabidopsis seeds.

A DE1 BINDING FACTOR 1-GLABRA2 module regulates rhamnogalacturonan I biosynthesis in Arabidopsis seed coat mucilage

The mucilage surrounding hydrated Arabidopsis thaliana seeds is a specialized extracellular matrix composed mainly of the pectic polysaccharide rhamnogalacturonan I (RG-I). Although, several genes responsible for RG-I biosynthesis have been identified, the transcriptional regulatory mechanisms controlling RG-I production remain largely unknown. Here we report that the trihelix transcription factor DE1 BINDING FACTOR 1 (DF1) is a key regulator of mucilage RG-I biosynthesis. RG-I biosynthesis is significantly reduced in loss-of-function mutants of DF1. DF1 physically interacts with GLABRA2 (GL2) and both proteins transcriptionally regulate the expression of the RG-I biosynthesis genes MUCILAGE MODIFIED 4 (MUM4) and GALACTURONOSYLTRANSFERASE-LIKE5 (GATL5). Through chromatin immunoprecipitation-quantitative PCR and transcriptional activation assays, we uncover a cooperative mechanism of the DF1-GL2 module in activating MUM4 and GATL5 expression, in which DF1 binds to the promoters of MUM4 and GATL5 through interacting with GL2 and facilitates the transcriptional activity of GL2. The expression of DF1 and GL2 is directly regulated by TRANSPARENT TESTA GLABRA2 (TTG2) and, in turn, DF1 directly represses the expression of TTG2. Taken together, our data reveal that the transcriptional regulation of mucilage RG-I biosynthesis involves a regulatory module, comprising DF1, GL2, and TTG2.

Expression Patterns and Functional Characterization of Arabidopsis Galactose Oxidase-Like Genes Suggest Specialized Roles for Galactose Oxidases in Plants

Galactose oxidases (GalOxs) are well-known enzymes that have been identified in several fungal species and characterized using structural and enzymatic approaches. However, until very recently, almost no information on their biological functions was available. The Arabidopsis (Arabidopsis thaliana) gene ruby particles in mucilage (RUBY) encodes a putative plant GalOx that is required for pectin cross-linking through modification of galactose (Gal) side chains and promotes cell-cell adhesion between seed coat epidermal cells. RUBY is one member of a family of seven putative GalOxs encoded in the Arabidopsis genome. To examine the function(s) of GalOxs in plants, we studied the remaining six galactose oxidase-like (GOXL) proteins. Like RUBY, four of these proteins (GOXL1, GOXL3, GOXL5 and GOXL6) were found to localize primarily to the apoplast, while GOXL2 and GOXL4 were found primarily in the cytoplasm. Complementation and GalOx assay data suggested that GOXL1, GOXL3 and possibly GOXL6 have similar biochemical activity to RUBY, whereas GOXL5 only weakly complemented and GOXL2 and GOXL4 showed no activity. Members of this protein family separated into four distinct clades prior to the divergence of the angiosperms. There have been recent duplications in Brassicaceae resulting in two closely related pairs of genes that have either retained similarity in expression (GOXL1 and GOXL6) or show expression divergence (GOXL3 and RUBY). Mutant phenotypes were not detected when these genes were disrupted, but their expression patterns suggest that these proteins may function in tissues that require mechanical reinforcements in the absence of lignification.

Pectin Modification in Seed Coat Mucilage by In Vivo Expression of Rhamnogalacturonan-I- and Homogalacturonan-Degrading Enzymes

The cell wall is essential for plant survival. Determining the relationship between cell wall structure and function using mutant analysis or overexpressing cell wall-modifying enzymes has been challenging due to the complexity of the cell wall and the appearance of secondary, compensatory effects when individual polymers are modified. In addition, viability of the plants can be severely impacted by wall modification. A useful model system for studying structure-function relationships among extracellular matrix components is the seed coat epidermal cells of Arabidopsis thaliana. These cells synthesize relatively simple, easily accessible, pectin-rich mucilage that is not essential for plant viability. In this study, we expressed enzymes predicted to modify polysaccharide components of mucilage in the apoplast of seed coat epidermal cells and explored their impacts on mucilage. The seed coat epidermal-specific promoter TESTA ABUNDANT2 (TBA2) was used to drive expression of these enzymes to avoid adverse effects in other parts of the plant. Mature transgenic seeds expressing Rhamnogalacturonate lyase A (RglA) or Rhamnogalacturonate lyase B (RglB) that degrade the pectin rhamnogalacturonan-I (RG-I), a major component of mucilage, had greatly reduced mucilage capsules surrounding the seeds and concomitant decreases in the monosaccharides that comprise the RG-I backbone. Degradation of the minor mucilage component homogalacturonan (HG) using the HG-degrading enzymes Pectin lyase A (PLA) or ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE2 (ADPG2) resulted in developing seed coat epidermal cells with disrupted cell-cell adhesion and signs of early cell death. These results demonstrate the feasibility of manipulating the seed coat epidermal cell extracellular matrix using a targeted genetic engineering approach.

Seed Mucilage: Biological Functions and Potential Applications in Biotechnology

In plants, the diaspore (seed dispersal unit) may include a seed coat and/or pericarp to protect the embryo and assist in dispersion. In many species, the seed coat and/or pericarp secrete a gelatinous mixture of cell wall polysaccharides known as mucilage. In several species, mucilage synthesis, secretion and modification have been studied extensively as model systems for the investigation of plant cell wall structure and function. Despite this, efforts toward understanding the role of mucilage have received less attention. Mucilage has been hypothesized to impact seed dispersal through interaction with soil, protecting the seed in the gut following ingestion by animals or affecting the ability of seeds to sink or float in water. Mucilage has been found to influence seed germination and seedling establishment, most often during abiotic stress, probably by maintaining seed hydration when water is scarce. Finally, mucilage has been documented to mediate interactions with various organisms. Advances in transgenic technology should enable the genetic modification of mucilage structure and function in crop plants. Cells synthesizing mucilage may also be a suitable platform for creating custom polysaccharides or proteins with industrial applications. Thus, in the near future, it is likely that research on seed mucilage will expand well beyond the current focus. Here we summarize our understanding of the biological functions of mucilage and provide an outlook on the future of mucilage research.

Asymmetric distribution of extracellular matrix proteins in seed coat epidermal cells of Arabidopsis is determined by polar secretion

Although asymmetric deposition of the plant extracellular matrix is critical for the normal functioning of many cell types, the molecular mechanisms establishing this asymmetry are not well understood. During differentiation, Arabidopsis seed coat epidermal cells deposit large amounts of pectin-rich mucilage asymmetrically to form an extracellular pocket between the plasma membrane and the outer tangential primary cell wall. At maturity, the mucilage expands on contact with water, ruptures the primary cell wall, and extrudes to encapsulate the seed. In addition to polysaccharides, mucilage contains secreted proteins including the β-galactosidase MUCILAGE MODIFIED 2 (MUM2). A functional chimeric protein where MUM2 was fused translationally with Citrine yellow fluorescent protein (Citrine) indicated that MUM2-Citrine fluorescence preferentially accumulates in the mucilage pocket concomitant with mucilage deposition and rapidly disappears when mucilage synthesis ceases. A secreted form of Citrine, secCitrine, showed a similar pattern of localization when expressed in developing seed coat epidermal cells. This result suggested that both the asymmetric localization and rapid decrease of fluorescence is not unique to MUM2-Citrine and may represent the default pathway for secreted proteins in this cell type. v-SNARE proteins were localized only in the membrane adjacent to the mucilage pocket, supporting the hypothesis that the cellular secretory apparatus is redirected and targets secretion to the outer periclinal apoplast during mucilage synthesis. In addition, mutation of ECHIDNA, a gene encoding a TGN-localized protein involved in vesicle targeting, causes misdirection of mucilage, MUM2 and v-SNARE proteins from the apoplast/plasma membrane to the vacuole/tonoplast. Western blot analyses suggested that the disappearance of MUM2-Citrine fluorescence at the end of mucilage synthesis is due to protein degradation and because several proteases have been identified in extruded seed mucilage. However, as mutation of these genes did not result in a substantial delay in MUM2-Citrine degradation and the timing of their expression and/or their intracellular localization were not consistent with a role in MUM2-Citrine disappearance, the mechanism underlying the abrupt decrease of MUM2-Citrine remains unclear.

Myxospermy Evolution in Brassicaceae: A Highly Complex and Diverse Trait with Arabidopsis as an Uncommon Model

The ability to extrude mucilage upon seed imbibition (myxospermy) occurs in several Angiosperm taxonomic groups, but its ancestral nature or evolutionary convergence origin remains misunderstood. We investigated seed mucilage evolution in the Brassicaceae family with comparison to the knowledge accumulated in Arabidopsis thaliana. The myxospermy occurrence was evaluated in 27 Brassicaceae species. Phenotyping included mucilage secretory cell morphology and topochemistry to highlight subtle myxospermy traits. In parallel, computational biology was driven on the one hundred genes constituting the so-called A. thaliana mucilage secretory cell toolbox to confront their sequence conservation to the observed phenotypes. Mucilage secretory cells show high morphology diversity; the three studied Arabidopsis species had a specific extrusion modality compared to the other studied Brassicaceae species. Orthologous genes from the A. thaliana mucilage secretory cell toolbox were mostly found in all studied species without correlation with the occurrence of myxospermy or even more sub-cellular traits. Seed mucilage may be an ancestral feature of the Brassicaceae family. It consists of highly diverse subtle traits, probably underlined by several genes not yet characterized in A. thaliana or by species-specific genes. Therefore, A. thaliana is probably not a sufficient reference for future myxospermy evo-devo studies.

StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development

Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.

ERF4 and MYB52 transcription factors play antagonistic roles in regulating homogalacturonan de-methylesterification in Arabidopsis seed coat mucilage

Homogalacturonan (HG), a component of pectin, is synthesized in the Golgi apparatus in its fully methylesterified form. It is then secreted into the apoplast where it is typically de-methylesterified by pectin methylesterases (PME). Secretion and de-esterification are critical for normal pectin function, yet the underlying transcriptional regulation mechanisms remain largely unknown. Here, we uncovered a mechanism that fine-tunes the degree of HG de-methylesterification (DM) in the mucilage that surrounds Arabidopsis thaliana seeds. We demonstrate that the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor (TF) ERF4 is a transcriptional repressor that positively regulates HG DM. ERF4 expression is confined to epidermal cells in the early stages of seed coat development. The adhesiveness of the erf4 mutant mucilage was decreased as a result of an increased DM caused by a decrease in PME activity. Molecular and genetic analyses revealed that ERF4 positively regulates HG DM by suppressing the expression of three PME INHIBITOR genes (PMEIs) and SUBTILISIN-LIKE SERINE PROTEASE 1.7 (SBT1.7). ERF4 shares common targets with the TF MYB52, which also regulates pectin DM. Nevertheless, the erf4-2 myb52 double mutant seeds have a wild-type mucilage phenotype. We provide evidence that ERF4 and MYB52 regulate downstream gene expression in an opposite manner by antagonizing each other's DNA-binding ability through a physical interaction. Together, our findings reveal that pectin DM in the seed coat is fine-tuned by an ERF4-MYB52 transcriptional complex.

Seed coat mucilages: Structural, functional/bioactive properties, and genetic information

Seed coat mucilages are mainly polysaccharides covering the outer layer of the seeds to facilitate seed hydration and germination, thereby improving seedling emergence and reducing seedling mortality. Four types of polysaccharides are found in mucilages including xylan, pectin, glucomannan, and cellulose. Recently, mucilages from flaxseed, yellow mustard seed, chia seed, and so on, have been used extensively in the areas of food, pharmaceutical, and cosmetics contributing to stability, texture, and appearance. This review, for the first time, addresses the similarities and differences in physicochemical properties, molecular structure, and functional/bioactive properties of mucilages among different sources; highlights their structure and function relationships; and systematically summarizes the related genetic information, aiming with the intent to explore the potential functions thereby extending their future industrial applications.

Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis

Lignans/neolignans are generally synthesized from coniferyl alcohol (CA) in the cinnamate/monolignol pathway by oxidation to generate the corresponding radicals with subsequent stereoselective dimerization aided by dirigent proteins (DIRs). Genes encoding oxidases and DIRs for neolignan biosynthesis have not been identified previously. In Arabidopsis thaliana, the DIR AtDP1/AtDIR12 plays an essential role in the 8-O-4' coupling in neolignan biosynthesis by unequivocal structural determination of the compound missing in the atdp1 mutant as a sinapoylcholine (SC)-conjugated neolignan, erythro-3-{4-[2-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-1-hydroxymethylethoxy]-3,5-dimethoxyphenyl}acryloylcholine. Phylogenetic analyses showed that AtDP1/AtDIR12 belongs to the DIR-a subfamily composed of DIRs for 8-8' coupling of monolignol radicals. AtDP1/AtDIR12 is specifically expressed in outer integument 1 cells in developing seeds. As a putative oxidase for neolignan biosynthesis, we focused on AtLAC5, a laccase gene coexpressed with AtDP1/AtDIR12. In lac5 mutants, the abundance of feruloylcholine (FC)-conjugated neolignans decreased to a level comparable to those in the atdp1 mutant. In addition, SC/FC-conjugated neolignans were missing in the seeds of mutants defective in SCT/SCPL19, an enzyme that synthesizes SC. These results strongly suggest that AtDP1/AtDIR12 and AtLAC5 are involved in neolignan biosynthesis via SC/FC. A tetrazolium penetration assay showed that seed coat permeability increased in atdp1 mutants, suggesting a protective role of neolignans in A. thaliana seeds.

HOMEODOMAIN GLABROUS2 regulates cellulose biosynthesis in seed coat mucilage by activating CELLULOSE SYNTHASE5

Numerous proteins involved in cellulose biosynthesis and assembly have been functionally characterized. Nevertheless, we have a limited understanding of the mechanisms underlying the transcriptional regulation of the genes that encode these proteins. Here, we report that HOMEODOMAIN GLABROUS2 (HDG2), a Homeobox-Leucine Zipper IV transcription factor, regulates cellulose biosynthesis in Arabidopsis (Arabidopsis thaliana) seed coat mucilage. HDG2 is a transcriptional activator with the transactivation domain located within its Leucine-Zipper domain. Transcripts of HDG2 were detected specifically in seed coat epidermal cells with peak expression at 10 d postanthesis. Disruptions of HDG2 led to seed coat mucilage with aberrant morphology due to a reduction in its crystalline cellulose content. Electrophoretic mobility shift and yeast one-hybrid assays, together with chromatin immunoprecipitation and quantitative PCR, provided evidence that HDG2 directly activates CELLULOSE SYNTHASE5 (CESA5) expression by binding to the L1-box cis-acting element in its promoter. Overexpression of CESA5 partially rescued the mucilage defects of hdg2-3. Together, our data suggest that HDG2 directly activates CESA5 expression and thus is a positive regulator of cellulose biosynthesis in seed coat mucilage.

Seed mucilage evolution: Diverse molecular mechanisms generate versatile ecological functions for particular environments

Plant myxodiasporous species have the ability to release a polysaccharidic mucilage upon imbibition of the seed (myxospermy) or the fruit (myxocarpy). This is a widespread capacity in angiosperms providing multiple ecological functions including higher germination efficiency under environmental stresses. It is unclear whether myxodiaspory has one or multiple evolutionary origins and why it was supposedly lost in several species. Here, we summarize recent advances on three main aspects of myxodiaspory. (a) It represents a combination of highly diverse traits at different levels of observation, ranging from the dual tissular origin of mucilage secretory cells to diverse mucilage polysaccharidic composition and ultrastructural organization. (b) An asymmetrical selection pressure is exerted on myxospermy-related genes that were first identified in Arabidopsis thaliana. The A. thaliana and the flax intra-species mucilage variants show that myxospermy is a fast-evolving trait due to high polymorphism in a few genes directly acting on mucilage establishment. In A. thaliana, these actors are downstream of a master regulatory complex and an original phylogenetic overview provided here illustrates that this complex has sequentially evolved after the common ancestor of seed plants and was fully established in the common ancestor of the rosid clade. (c) Newly identified myxodiaspory ecological functions indicate new perspectives such as soil microorganism control and plant establishment support.

TRANSPARENT TESTA GLABRA1, a Key Regulator in Plants with Multiple Roles and Multiple Function Mechanisms

TRANSPARENT TESTA GLABRA1 (TTG1) is a WD40 repeat protein. The phenotypes caused by loss-of-function of TTG1 were observed about half a century ago, but the TTG1 gene was identified only about twenty years ago. Since then, TTG1 has been found to be a plant-specific regulator with multiple roles and multiple functional mechanisms. TTG1 is involved in the regulation of cell fate determination, secondary metabolisms, accumulation of seed storage reserves, plant responses to biotic and abiotic stresses, and flowering time in plants. In some processes, TTG1 may directly or indirectly regulate the expression of downstream target genes via forming transcription activator complexes with R2R3 MYB and bHLH transcription factors. Whereas in other processes, TTG1 may function alone or interact with other proteins to regulate downstream target genes. On the other hand, the studies on the regulation of TTG1 are very limited. So far, only the B3-domain family transcription factor FUSCA3 (FUS3) has been found to regulate the expression of TTG1, phosphorylation of TTG1 affects its interaction with bHLH transcription factor TT2, and TTG1 proteins can be targeted for degradation by the 26S proteasome. Here, we provide an overview of TTG1, including the identification of TTG1, the functions of TTG1, the possible function mechanisms of TTG1, and the regulation of TTG1. We also proposed potential research directions that may shed new light on the regulation and functional mechanisms of TTG1 in plants.

A simple, non-toxic method for separating seeds based on density, and its application in isolating Arabidopsis thaliana seed oil mutants

PREMISE

Seed oil is an economically important trait in Brassica oilseed crops. A novel method was developed to isolate Arabidopsis thaliana seeds with altered oil content.

METHODS AND RESULTS

In A. thaliana, seed oil content is correlated with seed density, with high-oil seeds being less dense than wild type and tending to float in solution, and low-oil seeds being denser and tending to sink. In contrast to previous methods, which used toxic chemicals and density gradient centrifugation, different concentrations of calcium chloride (CaCl2) were employed to separate seeds without the need for centrifugation. The method was validated using known seed oil mutants, and 120,822 T-DNA mutagenized A. thaliana lines were then screened for novel seed density phenotypes.

CONCLUSIONS

A number of candidate mutants, as well as new alleles of two genes known to influence seed oil biosynthesis, were successfully isolated.

A small-scale fractionation pipeline for rapid analysis of seed mucilage characteristics

BACKGROUND

Myxospermy is a process by which the external surfaces of seeds of many plant species produce mucilage-a polysaccharide-rich gel with numerous fundamental research and industrial applications. Due to its functional properties the mucilage can be difficult to remove from the seed and established methods for mucilage extraction are often incomplete, time-consuming and unnecessarily wasteful of precious seed stocks.

RESULTS

Here we tested the efficacy of several established protocols for seed mucilage extraction and then downsized and adapted the most effective elements into a rapid, small-scale extraction and analysis pipeline. Within 4 h, three chemically- and functionally-distinct mucilage fractions were obtained from myxospermous seeds. These fractions were used to study natural variation and demonstrate structure-function links, to screen for known mucilage quality markers in a field trial, and to identify research and industry-relevant lines from a large mutant population.

CONCLUSION

The use of this pipeline allows rapid analysis of mucilage characteristics from diverse myxospermous germplasm which can contribute to fundamental research into mucilage production and properties, quality testing for industrial manufacturing, and progressing breeding efforts in myxospermous crops.

Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development

EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.

Assessing the utility of seed coat-specific promoters to engineer cell wall polysaccharide composition of mucilage

Polysaccharide composition of seed mucilage was successfully modified using three seed coat-specific promoters driving expression of genes encoding cell wall-modifying enzymes. Arabidopsis thaliana seed coat epidermal cells synthesize and secrete large quantities of mucilage, a specialized secondary cell wall composed of cellulose, hemicellulose, and pectin. The composition and structure of mucilage confers its unique properties of expansion, extrusion, and adherence. We are developing seed mucilage as a model to study the biochemical and biological consequences of manipulating cell wall polysaccharides in vivo using cell wall-modifying enzymes. To specifically engineer mucilage composition and avoid altering other cell types, seed coat-specific promoters are required. In this study, we investigated the ability of seed coat-specific promoters from three genes, TESTA-ABUNDANT2 (TBA2), PEROXIDASE36 (PER36), and MUCILAGE-MODIFIED4 (MUM4), to express the cell wall modifying β-galactosidase (BGAL)-encoding gene MUCILAGE-MODIFIED2 (MUM2) and complement the mum2 mutant. The strength of the three promoters relative to one another was found to vary by two to 250 fold, and correlated with their ability to rescue the mum2 mutant phenotype. The strongest of the three promoters, TBA2p, was then used to examine the ability of three MUM2 homologs to complement the mum2 extrusion and cell wall composition phenotypes. The degree of complementation was variable and correlated with the amino acid sequence similarity between the homologous gene products and MUM2. These data demonstrate that all three seed coat-specific promoters can drive expression of genes encoding carbohydrate-active enzymes in a spatial and temporal pattern sufficiently to modify polysaccharide composition in seed mucilage without obvious negative consequences to the rest of the plant.

Genome-Wide Identification of Direct Targets of the TTG1-bHLH-MYB Complex in Regulating Trichome Formation and Flavonoid Accumulation in Arabidopsis Thaliana

Extensive studies have shown that the MBW complex consisting of three kinds of regulatory proteins, MYB and basic helix–loop–helix (bHLH) transcription factors and a WD40 repeat protein, TRANSPARENT TESTA GLABRA1 (TTG1), acts in concert to promote trichome formation and flavonoid accumulation in Arabidopsis thaliana. TTG1 functions as an essential activator in these two biological processes. However, direct downstream targets of the TTG1-dependent MBW complex have not yet been obtained in the two biological processes at the genome-wide level in A. thaliana. In the present study, we found, through RNA sequencing and quantitative real-time PCR analysis, that a great number of regulatory and structural genes involved in both trichome formation and flavonoid accumulation are significantly downregulated in the young shoots and expanding true leaves of ttg1-13 plants. Post-translational activation of a TTG1-glucocorticoid receptor fusion protein and chromatin immunoprecipitation assays demonstrated that these downregulated genes are directly or indirectly targeted by the TTG1-dependent MBW complex in vivo during trichome formation and flavonoid accumulation. These findings further extend our understanding of the role of TTG1-dependent MBW complex in the regulation of trichome formation and flavonoid accumulation in A. thaliana.

Composition and physicochemical properties of outer mucilage from seeds of Arabidopsis natural accessions

Arabidopsis thaliana (Arabidopsis) seeds are myxospermous and release two layers of mucilage on imbibition. The outer layer can be extracted with water facilitating the analysis of its major constituent, polysaccharides. The composition and properties of outer mucilage have been determined for 306 natural accessions and six control genotypes to generate a data set comprising six traits measured in four biological replicates for each. Future exploitation of this data is possible in a range of analyses and should yield information concerning genetic diversity, underlying genetic factors and the biological function of mucilage as an adaptive trait.

Making glue from seeds and gums: Working with plant-based polymers to introduce students to plant biochemistry

Plants and plant products are key to the survival of life on earth. Despite this fact, the significance of plant biochemistry is often underrepresented in science curricula. We designed an innovative laboratory activity to engage students in learning about the biochemical properties of natural polymers produced by plants. The focus of the hands-on activity is on mucilages and gums, which contain complex polysaccharides that have applications in industry. The 1.5-h activity is organized into three laboratory exercises. It begins with a demonstration of the water absorption property of seed coat mucilage upon hydration of seeds from psyllium, a plant that is grown commercially for mucilage production. The second exercise involves microscopy of a variety of plant seeds stained with ruthenium red dye to visualize pectin polysaccharides of the seed mucilage. Students learn about phenotypic variation among plant species and how the seed coat mucilage is beneficial to keep seeds hydrated during germination. The third exercise highlights an industrial application of plant gums as adhesives. The students prepare edible glue made with gum arabic, a type of plant polymer from the dried exudate of the Acacia plant. This three-part activity has been implemented in conjunction with a Girls Researching Our World (GROW) summer workshop for sixth to eighth graders over a 4-year period. It may be adapted as a laboratory activity for students of all ages, for example, to enhance biochemistry education for high-school students or undergraduate non-majors. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):468-475, 2019.

Ectopic expression of the Aechmea fasciata APETALA2 gene AfAP2-2 reduces seed size and delays flowering in Arabidopsis

The Bromeliaceae family, which is distributed pantropically, is one of the most morphologically diverse families. Except for the edible pineapple (Ananas comosus), the vast majority of bromeliads cultivated worldwide are appreciated mainly for their ornamental value. As subtropical and tropical flowering plants, these bromeliads, among with Aechmea fasciata, have significant economic importance. However, the molecular mechanism of flowering in bromeliads remains unrevealed. In this study, an APETALA2 (AP2) homologue, AfAP2-2, which belongs to the AP2/ethylene response element binding protein (AP2/EREBP) transcription factor superfamily, was identified in A. fasciata. AfAP2-2 contains two conserved AP2 domains and is a nuclear-localized transactivator. The expression level of AfAP2-2 was predominantly higher in vegetative organs of the reproductive phase than in those of the vegetative phase. Ectopic expression of AfAP2-2 in Arabidopsis specifically delayed flowering in short-day (SD) conditions. Furthermore, the size and weight of seeds of AfAP2-2-overexpressing Arabidopsis plants were significantly reduced compared to those of the wild type (WT). Our findings suggest that AfAP2-2 might be a negative regulator of flowering and seed size and weight. These results may help facilitate the molecular breeding of bromeliads.

JcMYB1, a Jatropha R2R3MYB Transcription Factor Gene, Modulates Lipid Biosynthesis in Transgenic Plants

The lipid biosynthesis pathway in plants has been studied in detail; however, the factors that regulate the pathway at the transcription level are largely unknown. LEAFY COTYLEDON1 (LEC1), WRINKLED1 (WRI1) and FUSCA3 (FUS3) are considered master regulators to control seed oil content in Arabidopsis. Beside these master regulators, several other transcription factors that may regulate the pathway in plants are poorly studied. In the present work, we have shown the involvement of an uncharacterized Jatropha curcas R2R3MYB gene (JcMYB1) in seed oil biosynthesis. Seed oil analysis and expression profiling of fatty acid (FA) and triacylglycerol (TAG) biosynthetic genes in transgenic Arabidopsis and tobacco plants revealed that JcMYB1 enhances seed oil accumulation and alters FA composition by regulating the expression of endogenous pathway genes in transgenics. Using virus-induced gene silencing (VIGS) in Jatropha, we demonstrated that the suppression of JcMYB1 reduced lipid content with altered FA composition. Agro-infiltration and yeast one-hybrid assay results showed that JcMYB1 protein directly binds to the diacylglycerol acyltransferase1 (DGAT1) promoter, a rate-limiting enzyme of TAG biosynthesis, and activates its expression. These results suggested that JcMYB1 may augment the lipid content by regulating lipid biosynthetic genes. Additionally, manipulation of JcMYB1 in oil crop plants may be used for the potential improvement of oil production and quality.

MuSeeQ, a novel supervised image analysis tool for the simultaneous phenotyping of the soluble mucilage and seed morphometric parameters

BACKGROUND

The mucilage is a model to study the polysaccharide biosynthesis since it is produced in large amounts and composed of complex polymers. In addition, it is of great economic interest for its technical and nutritional value. A fast method for phenotyping the released mucilage and the seed morphometric parameters will be useful for fundamental, food, pharmaceutical and breeding researches. Current strategies to phenotype soluble mucilage are restricted to visual evaluations or are highly time-consuming.

RESULTS

Here, we developed a high-throughput phenotyping method for the simultaneous measurement of the soluble mucilage content released on a gel and the seed morphometric parameters. Within this context, we combined a biochemical assay and an open-source computer-aided image analysis tool, MuSeeQ. The biochemical assay consists in sowing seeds on an agarose medium containing the dye toluidine blue O, which specifically stains the mucilage once it is released on the gel. The second part of MuSeeQ is a macro developed in ImageJ allowing to quickly extract and analyse 11 morphometric data of seeds and their respective released mucilages. As an example, MuSeeQ was applied on a flax recombinant inbred lines population (previously screened for fatty acids content.) and revealed significant correlations between the soluble mucilage shape and the concentration of some fatty acids, e.g. C16:0 and C18:2. Other fatty acids were also found to correlate with the seed shape parameters, e.g. C18:0 and C18:2. MuSeeQ was then showed to be used for the analysis of other myxospermous species, including Arabidopsis thaliana and Camelina sativa.

CONCLUSIONS

MuSeeQ is a low-cost and user-friendly method which may be used by breeders and researchers for phenotyping simultaneously seeds of specific cultivars, natural variants or mutants and their respective soluble mucilage area released on a gel. The script of MuSeeQ and video tutorials are freely available at http://MuSeeQ.free.fr.

Biochemistry of complex glycan depolymerisation by the human gut microbiota

The human gut microbiota (HGM) makes an important contribution to health and disease. It is a complex microbial community of trillions of microbes with a majority of its members represented within two phyla, the Bacteroidetes and Firmicutes, although it also contains species of Actinobacteria and Proteobacteria. Reflecting its importance, the HGM is sometimes referred to as an 'organ' as it performs functions analogous to systemic tissues within the human host. The major nutrients available to the HGM are host and dietary complex carbohydrates. To utilise these nutrient sources, the HGM has developed elaborate, variable and sophisticated systems for the sensing, capture and utilisation of these glycans. Understanding nutrient acquisition by the HGM can thus provide mechanistic insights into the dynamics of this ecosystem, and how it impacts human health. Dietary nutrient sources include a wide variety of simple and complex plant and animal-derived glycans most of which are not degraded by enzymes in the digestive tract of the host. Here we review how various adaptive mechanisms that operate across the major phyla of the HGM contribute to glycan utilisation, focusing on the most complex carbohydrates presented to this ecosystem.

TRANSPARENT TESTA 4-mediated flavonoids negatively affect embryonic fatty acid biosynthesis in Arabidopsis

Flavonoids are involved in many physiological processes in plants. TRANSPARENT TESTA 4 (TT4) acts at the first step of flavonoid biosynthesis, and the loss of TT4 function causes a lack of flavonoid. Flavonoid deficiency is reportedly the main cause of increased fatty acid content in pale-coloured oilseeds, but details regarding the relationship between seed flavonoids and fatty acid biosynthesis are elusive. In this work, we applied a genetic strategy combined with biochemical and cytological assays to determine the effect of seed flavonoids on the biosynthesis of fatty acids in Arabidopsis thaliana. We showed that TT4-mediated flavonoids negatively affect embryonic fatty acid biosynthesis. A crossing experiment indicated that seed flavonoid biosynthesis and the impact of this process on fatty acid biosynthesis were controlled in a maternal line-dependent manner. Loss of TT4 function activated glycolysis in seed embryos, thereby enhancing fatty acid biosynthesis, but did not improve seed mucilage production. Moreover, loss of TT4 function reduced PIN-FORMED 4 expression and subsequently increased auxin accumulation in embryos. Pharmacologically and genetically elevated auxin levels enhanced seed fatty acid biosynthesis. These results indicated that flavonoids affect fatty acid biosynthesis by carbon source reallocation via regulation of WRINKLE1 and auxin transport.

Layers of regulation - Insights into the role of transcription factors controlling mucilage production in the Arabidopsis seed coat

A polysaccharide-rich mucilage is released from the seed coat epidermis of numerous plant species and has been intensively studied in the model plant Arabidopsis. This has led to the identification of a large number of genes involved in the synthesis, secretion and modification of cell wall polysaccharides such as pectin, hemicellulose and cellulose being identified. These genes include a small network of transcription factors (TFs) and transcriptional co-regulators, that not only regulate mucilage production, but epidermal cell differentiation and in some cases flavonoid biosynthesis in the internal endothelial layer of the seed coat. Here we focus on the function of these regulators and propose a simplified model where they are assigned to a hierarchical gene network with three regulatory levels (tiers) as a means of assisting in the interpretation of the complexity. We discuss limitations of current methodologies and highlight some of the problems associated with defining the function of TFs, particularly those that perform different functions in adjacent layers of the seed coat. We suggest approaches that should provide a more accurate picture of the function of transcription factors involved with mucilage production and release.

Arabidopsis ACYL-COA-BINDING PROTEIN1 interacts with STEROL C4-METHYL OXIDASE1-2 to modulate gene expression of homeodomain-leucine zipper IV transcription factors

Fatty acids (FAs) and sterols constitute building blocks of eukaryotic membranes and lipid signals. Co-regulation of FA and sterol synthesis is mediated by sterol regulatory element-binding proteins in animals but remains elusive in plants. We reported recently that Arabidopsis ACYL-COA-BINDING PROTEIN1 (ACBP1) modulates sterol synthesis via protein-protein interaction with STEROL C4-METHYL OXIDASE1-1 (SMO1-1). Herein, ACBP1 was demonstrated to co-express and interact with SMO1-2 by yeast two-hybrid, co-localization, pull-down, co-immunoprecipitation and β-glucuronidase assays. SMO1-2 silenced in acbp1 was used in phenotyping, GC-MS and expression profiling. ACBP1 co-expressed with SMO1-2 in embryo sacs, pollen and trichomes, corroborating with cooperative tissue-specific functions unseen with SMO1-1. SMO1-2 silencing in acbp1 impaired seed development, male and female gamete transmission, and pollen function. Genes encoding homeodomain-leucine zipper IV transcription factors (HDG5, HDG10, HDG11 and GLABRA2), which potentially bind phospholipids/sterols, were transcribed aberrantly. GLABRA2 targets (MYB23, MUM4 and PLDα1) were misregulated, causing glabra2-resembling trichome, seed coat mucilage and oil-accumulating phenotypes. Together with altered sterol and FA compositions upon ACBP1 mutation and/or SMO1-2 silencing, ACBP1-SMO1 interaction appears to mediate homeostatic co-regulation of FAs and sterols, which serve as lipid modulators for gene expression of homeodomain-leucine zipper IV transcription factors.