The use of abscisic acid analogues to analyse the substrate selectivity of UGT71B6, a UDP-glycosyltransferase ofArabidopsis thaliana

Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes

Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.

Persistence of Abscisic Acid Analogs in Plants: Chemical Control of Plant Growth and Physiology

Abscisic acid (ABA) is a plant hormone that regulates numerous plant processes, including plant growth, development, and stress physiology. ABA plays an important role in enhancing plant stress tolerance. This involves the ABA-mediated control of gene expression to increase antioxidant activities for scavenging reactive oxygen species (ROS). ABA is a fragile molecule that is rapidly isomerized by ultraviolet (UV) light and catabolized in plants. This makes it challenging to apply as a plant growth substance. ABA analogs are synthetic derivatives of ABA that alter ABA's functions to modulate plant growth and stress physiology. Modifying functional group(s) in ABA analogs alters the potency, selectivity to receptors, and mode of action (i.e., either agonists or antagonists). Despite current advances in developing ABA analogs with high affinity to ABA receptors, it remains under investigation for its persistence in plants. The persistence of ABA analogs depends on their tolerance to catabolic and xenobiotic enzymes and light. Accumulated studies have demonstrated that the persistence of ABA analogs impacts the potency of its effect in plants. Thus, evaluating the persistence of these chemicals is a possible scheme for a better prediction of their functionality and potency in plants. Moreover, optimizing chemical administration protocols and biochemical characterization is also critical in validating the function of chemicals. Lastly, the development of chemical and genetic controls is required to acquire the stress tolerance of plants for multiple different uses.

Molecular and genetic analyses revealed the phytotoxicity of perfluorobutane sulfonate

Perfluorobutane sulfonate (PFBS) has oily and hydrophobic characteristics similar to those of perfluorooctane sulfonic acid (PFOS), which is an environmental organic pollutant and has gradually become the main substitute for PFOS in industry. Several studies have revealed the potential toxicity of PFBS in animals. PFBS can be taken up and accumulate in plants; however, whether and how PFBS affects plant growth remain largely unclear. A low concentration of PFBS did not affect plant growth, indicating that it had higher environmental safety than other perfluorinated compounds; however, a high concentration of PFBS (>1 mM) markedly inhibited primary root growth in Arabidopsis thaliana. Subsequently, we investigated the molecular mechanisms underlying plant growth mediated by high concentrations of PFBS. First, a genome-wide transcriptomic analysis revealed that PFBS altered the expression of genes associated with phytohormone signaling pathways. Combining physio-biochemical and genetic analyses, we next demonstrated that PFBS reduced the contents of indole-3-acetic acid (IAA) and abscisic acid (ABA), and disrupted the two signaling pathways in plants, finally inhibiting root growth. Moreover, a high concentration of PFBS also inhibited photosynthesis by comprehensively repressing the expression of genes related to the Calvin cycle and the photosynthetic apparatus. Such an understanding is helpful for elucidating the phytotoxicity of PFBS and provides a new strategy for toxicology research on organic pollutants in plants.

Genome Wide Analysis of Family-1 UDP Glycosyltransferases in Populus trichocarpa Specifies Abiotic Stress Responsive Glycosylation Mechanisms

Populus trichocarpa (Black cottonwood) is a dominant timber-yielding tree that has become a notable model plant for genome-level insights in forest trees. The efficient transport and solubility of various glycoside-associated compounds is linked to Family-1 UDP-glycosyltransferase (EC 2.4.1.x; UGTs) enzymes. These glycosyltransferase enzymes play a vital role in diverse plant functions, such as regulation of hormonal homeostasis, growth and development (seed, flower, fiber, root, etc.), xenobiotic detoxification, stress response (salt, drought, and oxidative), and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of the P. trichocarpa genome that identified 191 putative UGTs distributed across all chromosomes (with the exception of chromosome 20) based on 44 conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. Phylogenetic analysis of the 191 Populus UGTs together with 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 16 major groups (A–P). Whole-genome duplication events were the dominant pattern of duplication among UGTs in Populus. A well-conserved intron insertion was detected in most intron-containing UGTs across eight examined eudicots, including Populus. Most of the UGT genes were found preferentially expressed in leaf and root tissues in general. The regulation of putative UGT expression in response to drought, salt and heat stress was observed based on microarray and available RNA sequencing datasets. Up- and down-regulated UGT expression models were designed, based on transcripts per kilobase million values, confirmed their maximally varied expression under drought, salt and heat stresses. Co-expression networking of putative UGTs indicated their maximum co-expression with cytochrome P450 genes involved in triterpenoid biosynthesis. Our results provide an important resource for the identification of functional UGT genes to manipulate abiotic stress responsive glycosylation in Populus.

Structure-function relationship of terpenoid glycosyltransferases from plants

Covering: up to 2021Terpenoids are physiologically active substances that are of great importance to humans. Their physicochemical properties are modified by glycosylation, in terms of polarity, volatility, solubility and reactivity, and their bioactivities are altered accordingly. Significant scientific progress has been made in the functional study of glycosylated terpenes and numerous plant enzymes involved in regio- and enantioselective glycosylation have been characterized, a reaction that remains chemically challenging. Crucial clues to the mechanism of terpenoid glycosylation were recently provided by the first crystal structures of a diterpene glycosyltransferase UGT76G1. Here, we review biochemically characterized terpenoid glycosyltransferases, compare their functions and primary structures, discuss their acceptor and donor substrate tolerance and product specificity, and elaborate features of the 3D structures of the first terpenoid glycosyltransferases from plants.

Contrasting dynamics in abscisic acid metabolism in different Fragaria spp. during fruit ripening and identification of the enzymes involved

Abscisic acid (ABA) is a key hormone in non-climacteric Fragaria spp, regulating multiple physiological processes throughout fruit ripening. Its concentration increases during ripening, and it promotes fruit (receptacle) development. However, its metabolism in the fruit is largely unknown. We analyzed the concentrations of ABA and its catabolites at different developmental stages of strawberry ripening in diploid and octoploid genotypes and identified two functional ABA-glucosyltransferases (FvUGT71A49 and FvUGT73AC3) and two regiospecific ABA-8'-hydroxylases (FaCYP707A4a and FaCYP707A1/3). ABA-glucose ester content increased during ripening in diploid F. vesca varieties but decreased in octoploid F.×ananassa. Dihydrophaseic acid content increased throughout ripening in all analyzed receptacles, while 7'-hydroxy-ABA and neo-phaseic acid did not show significant changes during ripening. In the studied F. vesca varieties, the receptacle seems to be the main tissue for ABA metabolism, as the concentration of ABA and its metabolites in the receptacle was generally 100 times higher than in achenes. The accumulation patterns of ABA catabolites and transcriptomic data from the literature show that all strawberry fruits produce and metabolize considerable amounts of the plant hormone ABA during ripening, which is therefore a conserved process, but also illustrate the diversity of this metabolic pathway which is species, variety, and tissue dependent.

UDP-Sugar Producing Pyrophosphorylases: Distinct and Essential Enzymes With Overlapping Substrate Specificities, Providing de novo Precursors for Glycosylation Reactions

Nucleotide sugars are the key precursors for all glycosylation reactions and are required both for oligo- and polysaccharides synthesis and protein and lipid glycosylation. Among all nucleotide sugars, UDP-sugars are the most important precursors for biomass production in nature (e.g., synthesis of cellulose, hemicellulose, and pectins for cell wall production). Several recent studies have already suggested a potential role for UDP-Glc in plant growth and development, and UDP-Glc has also been suggested as a signaling molecule, in addition to its precursor function. In this review, we will cover primary mechanisms of formation of UDP-sugars, by focusing on UDP-sugar metabolizing pyrophosphorylases. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP-N-acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. Earlier studies with transgenic plants have revealed that each of the pyrophosphorylases is essential for plant survival, and their loss or a decrease in activity results in reproductive impairment. This constitutes a problem when studying exact in vivo roles of the enzymes using classical reverse genetics approaches. Thus, strategies involving the use of specific inhibitors (reverse chemical genetics) are also discussed. Further characterization of the properties/roles of pyrophosphorylases should address fundamental questions dealing with mechanisms and control of carbohydrate synthesis and may allow to identify targets for manipulation of biomass production in plants.

Transcriptome analysis of Chinese bayberry (Myrica rubra Sieb. et Zucc.) fruit treated with heat and 1-MCP

Chinese bayberry (Myrica rubra Sieb. et Zucc.) is a typical fruit tree grown in the hilly region of Southern China. The fruit is sensitive to storage and transportation conditions and presents a major problem in its commercialization. The present study was conducted to investigate the regulation of gene expression involved in plant hormone signaling pathway in the Chinese bayberry with different treatments of heat and 1-methylcyclopene (1-MCP) during postharvest storage. In one treatment group (HM group), we exposed Chinese bayberry fruit to 48 °C for 10 min and then sealed them in a desiccator with 5 μl·L^-1 of 1-MCP for 24 h at 20 °C, followed by storage at 10 °C. Another group (CK group) was directly stored at 10 °C without any prior treatment. Samples of fruit were collected every three days, at 3, 6, 9, 12 and 15 d (CK3, CK6, CK9, CK12 and CK15; and HM3, HM6, HM9, HM12, and HM15, respectively). The decay index of fruits in the CK group increased after six days of storage but did not increase until nine days of storage in the HM group. Superoxide dismutase (SOD) activity in the CK group was shown a downtrend during storage, and almost no fluctuation from six days. In the HM group, SOD activity increased after three days, but decreased sharply after six days storage. Besides, peroxidase (POD) and catalase (CAT) activities were shown the similar trend during the storage, both of them first increased and then decreased form the six days of storage. These physiological data indicated that the sixth day is a crucial time during the storage of Chinese bayberry treated with heat and 1-MCP. Therefore, the transcriptome libraries were constructed from CK0, CK6, HM6 group, respectively. The analysis of top 20 KEGG pathways showed that most differentially expressed genes were involved in the biosynthesis of secondary metabolites, particularly flavonoids and flavanols biosynthesis, in CK0 vs. CK6 and CK0 vs. HM6. However, the top three KEGG pathways in CK6 vs. HM6 were the ribosome, RNA transport and endocytosis during the storage. Expression of six ethylene receptor (ETR) genes and four ethylene-responsive transcription factor (ERF) genes were activated at transcriptional level during the postharvest stage and were decreased by heat and 1-MCP treatment, and serine/threonine-protein kinase 1 (CTR1) was also repressed by treatment. Abscisic acid (ABA) -responsive element binding factor (ABF) gene, auxin-responsive GH3 gene and transcription factor MYC2 gene also showed similar expression pattern with ethylene pathway genes. These results might improve our understanding of the mechanisms of heat and 1-MCP inhibition of fruit postharvest physiology and prolongation of fruit shelf life.

Comparative Genomic and Transcriptomic Analyses of Family-1 UDP Glycosyltransferase in Prunus Mume

Glycosylation mediated by Family-1 UDP-glycosyltransferases (UGTs) plays crucial roles in plant growth and adaptation to various stress conditions. Prunus mume is an ideal crop for analyzing flowering for its early spring flowering characteristics. Revealing the genomic and transcriptomic portfolio of the UGT family in P. mume, a species in which UGTs have not yet been investigated, is therefore important. In this study, 130 putative UGT genes were identified and phylogenetically clustered into 14 groups. These PmUGTs were distributed unevenly across eight chromosomes and 32 tandem duplication and 8 segmental duplication pairs were revealed. A highly conserved intron insertion event was revealed on the basis of intron/exon patterns within PmUGTs. According to RNA-seq data, these PmUGTs were specifically expressed in different tissues and during the bud dormancy process. In addition, we confirmed the differential expression of some representative genes in response to abscisic acid treatment. Our results will provide important information on the UGT family in P. mume that should aid further characterization of their biological roles in response to environmental stress.

Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation

In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.

Suppressing ABA uridine diphosphate glucosyltransferase (SlUGT75C1) alters fruit ripening and the stress response in tomato

Abscisic acid (ABA) glucose conjugation mediated by uridine diphosphate glucosyltransferases (UGTs) is an important pathway in regulating ABA homeostasis. In the present study, we investigated three tomato SlUGTs that are highly expressed in fruit during ripening, and these SlUGTs were localized to the cytoplasm and cell nucleus. Among these three UGTs, SlUGT75C1 catalyzes the glucosylation of both ABA and IAA in vitro; SlUGT76E1 can only catalyze the conjugation of ABA; and SlUGT73C4 cannot glycosylate either ABA or IAA. Therefore, SlUGT75C1 was selected for further investigation. SlUGT75C1 RNA interference significantly up-regulated the expression level of SlCYP707A2, which encodes an ABA 8'-hydroxylase but did not affect the expression of SlNCED1, which encodes a key enzyme in ABA biosynthesis. Suppression of SlUGT75C1 significantly accelerated fruit ripening by enhancing ABA levels and promoting the early release of ethylene. SlUGT75C1-RNAi altered the expression of fruit ripening genes (genes involved in ethylene release and cell wall catabolism). SlUGT75C1-RNAi seeds showed delayed germination and root growth compared with wild-type as well as increased sensitivity to exogenous ABA. SlUGT75C1-RNAi plants were also more resistant to drought stress. These results demonstrated that SlUGT75C1 plays a crucial role in ABA-mediated fruit ripening, seed germination, and drought responses in tomato.

High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites

Here, we report potential transcripts involved in the biosynthesis of therapeutic metabolites in Swertia japonica , the first report of transcriptome assembly, and characterization of the medicinal plant from Swertia genus. Swertia genus, representing over 170 plant species including herbs such as S. chirata, S. hookeri, S. longifolia, S. japonica, among others, have been used as the traditional medicine in China, India, Korea, and Japan for thousands of years. Due to the lack of genomic and transcriptomic resources, little is known about the molecular basis involved in the biosynthesis of characteristic key bioactive metabolites. Here, we performed deep-transcriptome sequencing for the aerial tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 bps. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding 81,729 unigenes having an average length of 884 bps and N50 value of 1452 bps, of which 46,963 unigenes were annotated based on the sequence similarity against NCBI-nr protein database. Annotation of transcriptome assembly resulted in the identification of putative genes encoding all enzymes from the key therapeutic metabolite biosynthesis pathways. Transcript abundance analysis, gene ontology enrichment analysis, and KEGG pathway enrichment analysis revealed metabolic processes being up-regulated in the aerial tissues with respect to the roots of S. japonica. We also identified 37 unigenes as potential candidates involved in the glycosylation of bioactive metabolites. Being the first report of transcriptome assembly and annotation for any of the Swertia species, this study will be a valuable resource for future investigations on the biosynthetic pathways of therapeutic metabolites and their regulations.

Plant secondary metabolism linked glycosyltransferases: An update on expanding knowledge and scopes

The multigene family of enzymes known as glycosyltransferases or popularly known as GTs catalyze the addition of carbohydrate moiety to a variety of synthetic as well as natural compounds. Glycosylation of plant secondary metabolites is an emerging area of research in drug designing and development. The unsurpassing complexity and diversity among natural products arising due to glycosylation type of alterations including glycodiversification and glycorandomization are emerging as the promising approaches in pharmacological studies. While, some GTs with broad spectrum of substrate specificity are promising candidates for glycoengineering while others with stringent specificity pose limitations in accepting molecules and performing catalysis. With the rising trends in diseases and the efficacy/potential of natural products in their treatment, glycosylation of plant secondary metabolites constitutes a key mechanism in biogeneration of their glycoconjugates possessing medicinal properties. The present review highlights the role of glycosyltransferases in plant secondary metabolism with an overview of their identification strategies, catalytic mechanism and structural studies on plant GTs. Furthermore, the article discusses the biotechnological and biomedical application of GTs ranging from detoxification of xenobiotics and hormone homeostasis to the synthesis of glycoconjugates and crop engineering. The future directions in glycosyltransferase research should focus on the synthesis of bioactive glycoconjugates via metabolic engineering and manipulation of enzyme's active site leading to improved/desirable catalytic properties. The multiple advantages of glycosylation in plant secondary metabolomics highlight the increasing significance of the GTs, and in near future, the enzyme superfamily may serve as promising path for progress in expanding drug targets for pharmacophore discovery and development.

RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis

The Panax genus has been a source of natural medicine, benefitting human health over the ages, among which the Panax japonicus represents an important species. Our understanding of several key pathways and enzymes involved in the biosynthesis of ginsenosides, a pharmacologically active class of metabolites and a major chemical constituents of the rhizome extracts from the Panax species, are limited. Limited genomic information, and lack of studies on comparative transcriptomics across the Panax species have restricted our understanding of the biosynthetic mechanisms of these and many other important classes of phytochemicals. Herein, we describe Illumina based RNA sequencing analysis to characterize the transcriptome and expression profiles of genes expressed in the five tissues of P. japonicus, and its comparison with other Panax species. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profiling, and gene ontology enrichment analysis for five tissues of P. japonicus showed that although overall processes were evenly conserved across all tissues. However, each tissue was characterized by several unique unigenes with the leaves showing the most unique unigenes among the tissues studied. A comparative analysis of the P. japonicus transcriptome assembly with publically available transcripts from other Panax species, namely, P. ginseng, P. notoginseng, and P. quinquefolius also displayed high sequence similarity across all Panax species, with P. japonicus showing highest similarity with P. ginseng. Annotation of P. japonicus transcriptome resulted in the identification of putative genes encoding all enzymes from the triterpene backbone biosynthetic pathways, and identified 24 and 48 unigenes annotated as cytochrome P450 (CYP) and glycosyltransferases (GT), respectively. These CYPs and GTs annotated unigenes were conserved across all Panax species and co-expressed with other the transcripts involved in the triterpenoid backbone biosynthesis pathways. Unigenes identified in this study represent strong candidates for being involved in the triterpenoid saponins biosynthesis, and can serve as a basis for future validation studies.

Functional Characterization and Substrate Promiscuity of UGT71 Glycosyltransferases from Strawberry (Fragaria × ananassa)

Glycosylation determines the complexity and diversity of plant natural products. To characterize fruit ripening-related UDP-dependent glycosyltransferases (UGTs) functionally in strawberry, we mined the publicly available Fragaria vesca genome sequence and found 199 putative UGT genes. Candidate UGTs whose expression levels were strongly up-regulated during fruit ripening were cloned from F.×ananassa and six were successfully expressed in Escherichia coli and biochemically characterized. UGT75T1 showed very strict substrate specificity and glucosylated only galangin out of 33 compounds. The other recombinant enzymes exhibited broad substrate tolerance, accepting numerous flavonoids, hydroxycoumarins, naphthols and the plant hormone, (+)-S-abscisic acid (ABA). UGT71W2 showed the highest activity towards 1-naphthol, while UGT71A33, UGT71A34a/b and UGT71A35 preferred 3-hydroxycoumarin and formed 3- and 7-O-glucosides as well as a diglucoside from flavonols. Screening of a strawberry physiological aglycone library identified kaempferol, quercetin, ABA and three unknown natural compounds as putative in planta substrates of UGT71A33, UGT71A34a and UGT71W2. Metabolite analyses of RNA interference (RNAi)-mediated silenced fruits demonstrated that UGT71W2 contributes to the glycosylation of flavonols, xenobiotics and, to a minor extent, of ABA, in planta. The study showed that both specialist and generalist UGTs were expressed during strawberry fruit ripening and the latter were probably not restricted to only one function in plants.

A transcript profiling approach reveals an abscisic acid-specific glycosyltransferase (UGT73C14) induced in developing fiber of Ligon lintless-2 mutant of cotton (Gossypium hirsutum L.)

Ligon lintless-2, a monogenic dominant cotton (Gossypium hirsutum L.) fiber mutation, causing extreme reduction in lint fiber length with no pleiotropic effects on vegetative growth, represents an excellent model system to study fiber elongation. A UDP-glycosyltransferase that was highly expressed in developing fibers of the mutant Ligon lintless-2 was isolated. The predicted amino acid sequence showed ~53% similarity with Arabidopsis UGT73C sub-family members and the UDP-glycosyltransferase was designated as UGT73C14. When expressed in Escherichia coli as a recombinant protein with a maltose binding protein tag, UGT73C14 displayed enzymatic activity toward ABA and utilized UDP-glucose and UDP-galactose as the sugar donors. The recombinant UGT73C14 converted natural occurring isoform (+)-cis, trans-ABA better than (+)-trans, trans-ABA and (-)-cis, trans-ABA. Transgenic Arabidopsis plants constitutively overexpressing UGT73C14 did not show phenotypic changes under standard growth conditions. However, the increased glycosylation of ABA resulted in phenotypic changes in post-germinative growth and seedling establishment, confirming in vivo activity of UGT73C14 for ABA. This suggests that the expression level of UGT73C14 is regulated by the observed elevated levels of ABA in developing fibers of the Li₂ mutant line and may be involved in the regulation of ABA homeostasis.

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.

Conjugates of abscisic acid, brassinosteroids, ethylene, gibberellins, and jasmonates

Phytohormones, including auxins, abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellins, and jasmonates, are involved in all aspects of plant growth, and developmental processes as well as environmental responses. However, our understanding of hormonal homeostasis is far from complete. Phytohormone conjugation is considered as a part of the mechanism to control cellular levels of these compounds. Active phytohormones are changed into multiple forms by acylation, esterification or glycosylation, for example. It seems that conjugated compounds could serve as pool of inactive phytohormones that can be converted to active forms by de-conjugation reactions. Some conjugates are thought to be temporary storage forms, from which free active hormones can be released after hydrolysis. It is also believed that conjugation serves functions, such as irreversible inactivation, transport, compartmentalization, and protection against degradation. The nature of abscisic acid, brassinosteroid, ethylene, gibberellin, and jasmonate conjugates is discussed.

ABA 9'-hydroxylation is catalyzed by CYP707A in Arabidopsis

Abscisic acid (ABA) catabolism is important for regulating endogenous ABA levels. To date, most effort has focused on catabolism of ABA to phaseic acid (PA), which is generated spontaneously after 8'-hydroxylation of ABA by cytochrome P450s in the CYP707A subfamily. Neophaseic acid (neoPA) is another well-documented ABA catabolite that is produced via ABA 9'-hydroxylation, but the 9'-hydroxylase has not yet been defined. Here, we show that endogenous neoPA levels are reduced in loss-of-function mutants defective in CYP707A genes. In addition, in planta levels of both neoPA and PA are reduced after treatment of plants with uniconazole-P, a P450 inhibitor. These lines of evidence suggest that CYP707A genes also encode the 9'-hydroxylase required for neoPA synthesis. To test this, in vitro enzyme assays using microsomal fractions from CYP707A-expressing yeast strains were conducted and these showed that all four Arabidopsis CYP707As are 9'-hydroxylases, although this activity is minor. Collectively, our results demonstrate that ABA 9'-hydroxylation is catalyzed by CYP707As as a side reaction.

A genomic approach to isoflavone biosynthesis in kudzu (Pueraria lobata)

Roots of kudzu (Pueraria lobata) are a rich source of isoflavone O- and C-glycosides. Although O-glycosylation of (iso)flavonoids has been well characterized at the molecular level, no plant isoflavonoid C-glycosyltransferase genes have yet been isolated. To address the biosynthesis of kudzu isoflavonoids, we generated 6,365 high-quality expressed sequence tags (ESTs) from a subtraction cDNA library constructed using RNA from roots that differentially accumulate puerarin. The ESTs were clustered into 722 TCs and 3,913 singletons, from which 15 family I glycosyltransferases (UGTs) were identified. Hierarchical clustering analysis of the expression patterns of these UGTs with isoflavone synthase (IFS) in a range of tissues identified UGTs with potential functions in isoflavone glycosylation. The open reading frames of these UGTs were expressed in E. coli for functional analysis, and one was shown to preferentially glycosylate isoflavones at the 7-O-position. In addition, ESTs corresponding to chalcone synthase, chalcone reductase, chalcone isomerase (CHI) and 2-hydroxyisoflavanone dehydratase were identified. Recombinant CHI proteins had high activities with both 6'-deoxy- and 6'-hydroxy chalcones, typical of Type II CHIs. Establishment of this EST database and identification of genes associated with kudzu isoflavone biosynthesis and glycosylation provide a new resource for metabolic engineering of bioactive kudzu isoflavones.

Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism

Until recently, most studies on the role of hormones in plant-pathogen interactions focused on salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). It is now clear that pathogen-induced modulation of signaling via other hormones contributes to virulence. A picture is emerging of complex crosstalk and induced hormonal changes that modulate disease and resistance, with outcomes dependent on pathogen lifestyles and the genetic constitution of the host. Recent progress has revealed intriguing similarities between hormone signaling mechanisms, with gene induction responses often achieved by derepression. Here, we report on recent advances, updating current knowledge on classical defense hormones SA, JA, and ET, and the roles of auxin, abscisic acid (ABA), cytokinins (CKs), and brassinosteroids in molding plant-pathogen interactions. We highlight an emerging theme that positive and negative regulators of these disparate hormone signaling pathways are crucial regulatory targets of hormonal crosstalk in disease and defense.

Perturbation of indole-3-butyric acid homeostasis by the UDP-glucosyltransferase UGT74E2 modulates Arabidopsis architecture and water stress tolerance

Reactive oxygen species and redox signaling undergo synergistic and antagonistic interactions with phytohormones to regulate protective responses of plants against biotic and abiotic stresses. However, molecular insight into the nature of this crosstalk remains scarce. We demonstrate that the hydrogen peroxide-responsive UDP-glucosyltransferase UGT74E2 of Arabidopsis thaliana is involved in the modulation of plant architecture and water stress response through its activity toward the auxin indole-3-butyric acid (IBA). Biochemical characterization of recombinant UGT74E2 demonstrated that it strongly favors IBA as a substrate. Assessment of indole-3-acetic acid (IAA), IBA, and their conjugates in transgenic plants ectopically expressing UGT74E2 indicated that the catalytic specificity was maintained in planta. In these transgenic plants, not only were IBA-Glc concentrations increased, but also free IBA levels were elevated and the conjugated IAA pattern was modified. This perturbed IBA and IAA homeostasis was associated with architectural changes, including increased shoot branching and altered rosette shape, and resulted in significantly improved survival during drought and salt stress treatments. Hence, our results reveal that IBA and IBA-Glc are important regulators of morphological and physiological stress adaptation mechanisms and provide molecular evidence for the interplay between hydrogen peroxide and auxin homeostasis through the action of an IBA UGT.

Karrikins discovered in smoke trigger Arabidopsis seed germination by a mechanism requiring gibberellic acid synthesis and light

Discovery of the primary seed germination stimulant in smoke, 3-methyl-2H-furo[2,3-c]pyran-2-one (KAR1), has resulted in identification of a family of structurally related plant growth regulators, karrikins. KAR1 acts as a key germination trigger for many species from fire-prone, Mediterranean climates, but a molecular mechanism for this response remains unknown. We demonstrate that Arabidopsis (Arabidopsis thaliana), an ephemeral of the temperate northern hemisphere that has never, to our knowledge, been reported to be responsive to fire or smoke, rapidly and sensitively perceives karrikins. Thus, these signaling molecules may have greater significance among angiosperms than previously realized. Karrikins can trigger germination of primary dormant Arabidopsis seeds far more effectively than known phytohormones or the structurally related strigolactone GR-24. Natural variation and depth of seed dormancy affect the degree of KAR1 stimulation. Analysis of phytohormone mutant germination reveals suppression of KAR1 responses by abscisic acid and a requirement for gibberellin (GA) synthesis. The reduced germination of sleepy1 mutants is partially recovered by KAR1, which suggests that germination enhancement by karrikin is only partly DELLA dependent. While KAR1 has little effect on sensitivity to exogenous GA, it enhances expression of the GA biosynthetic genes GA3ox1 and GA3ox2 during seed imbibition. Neither abscisic acid nor GA levels in seed are appreciably affected by KAR1 treatment prior to radicle emergence, despite marked differences in germination outcome. KAR1 stimulation of Arabidopsis germination is light-dependent and reversible by far-red exposure, although limited induction of GA3ox1 still occurs in the dark. The observed requirements for light and GA biosynthesis provide the first insights into the karrikin mode of action.

Identification and characterization of an Ipomoea nil glucosyltransferase which metabolizes some phytohormones

A glucosyltransferase gene InGTase1 was identified from the immature seeds of morning glory (Ipomoea nil), whose product shows a broad substrate-preference, including that of some phytohormones. When 2-trans-abscisic acid, indole-3-acetic acid, salicylic acid (SA) or (+/-)-jasmonic acid was reacted with InGTase1 and UDP-[(14)C]-glucose, each (14)C-labeled compound with high polarity was detected after thin layer chromatography. SA metabolites were identified as SA glucosyl ester by using (1)H NMR and GC/MS. Detailed substrate-preferences of InGTase1 were examined with some analogous compounds, which elucidated that the arm length and/or orientation of a carboxyl group of the compounds or its surrounding electron density severely affected the enzymatic activity. The broad substrate-preference will greatly contribute to the synthesis of various glucoconjugates.

Transcription analysis of arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence

A comparative transcriptome analysis for successive stages of Arabidopsis (Arabidopsis thaliana) developmental leaf senescence (NS), darkening-induced senescence of individual leaves attached to the plant (DIS), and senescence in dark-incubated detached leaves (DET) revealed many novel senescence-associated genes with distinct expression profiles. The three senescence processes share a high number of regulated genes, although the overall number of regulated genes during DIS and DET is about 2 times lower than during NS. Consequently, the number of NS-specific genes is much higher than the number of DIS- or DET-specific genes. The expression profiles of transporters (TPs), receptor-like kinases, autophagy genes, and hormone pathways were analyzed in detail. The Arabidopsis TPs and other integral membrane proteins were systematically reclassified based on the Transporter Classification system. Coordinate activation or inactivation of several genes is observed in some TP families in all three or only in individual senescence types, indicating differences in the genetic programs for remobilization of catabolites. Characteristic senescence type-specific differences were also apparent in the expression profiles of (putative) signaling kinases. For eight hormones, the expression of biosynthesis, metabolism, signaling, and (partially) response genes was investigated. In most pathways, novel senescence-associated genes were identified. The expression profiles of hormone homeostasis and signaling genes reveal additional players in the senescence regulatory network.

Use of the glucosyltransferase UGT71B6 to disturb abscisic acid homeostasis in Arabidopsis thaliana

A glucosyltransferase (GT) of Arabidopsis, UGT71B6, recognizing the naturally occurring enantiomer of abscisic acid (ABA) in vitro, has been used to disturb ABA homeostasis in planta. Transgenic plants constitutively overexpressing UGT71B6 (71B6-OE) have been analysed for changes in ABA and the related ABA metabolites abscisic acid glucose ester (ABA-GE), phaseic acid (PA), dihydrophaseic acid (DPA), 7'-hydroxyABA and neo-phaseic acid. Overexpression of the GT led to massive accumulation of ABA-GE and reduced levels of the oxidative metabolites PA and DPA, but had marginal effect on levels of free ABA. The control of ABA homeostasis, as reflected in levels of the different metabolites, differed in the 71B6-OEs whether the plants were grown under standard conditions or subjected to wilt stress. The impact of increased glucosylation of ABA on ABA-related phenotypes has also been assessed. Increased glucosylation of ABA led to phenotypic changes in post-germinative growth. The use of two structural analogues of ABA, known to have biological activity but to differ in their capacity to act as substrates for 71B6 in vitro, confirmed that the phenotypic changes arose specifically from the increased glucosylation caused by overexpression of 71B6. The phenotype and profile of ABA and related metabolites in a knockout line of 71B6, relative to wild type, has been assessed during Arabidopsis development and following stress treatments. The lack of major changes in these parameters is discussed in the context of functional redundancy of the multigene family of GTs in Arabidopsis.

Glycosyltransferases of lipophilic small molecules

Glycosyltransferases of small molecules transfer sugars to a wide range of acceptors, from hormones and secondary metabolites to biotic and abiotic chemicals and toxins in the environment. The enzymes are encoded by large multigene families and can be identified by a signature motif in their primary sequence, which classifies them as a subset of Family 1 glycosyltransferases. The transfer of a sugar onto a lipophilic acceptor changes its chemical properties, alters its bioactivity, and enables access to membrane transporter systems. In vitro studies have shown that a single gene product can glycosylate multiple substrates of diverse origins; multiple enzymes can also glycosylate the same substrate. These features suggest that in a cellular context, substrate availability is a determining factor in enzyme function, and redundancy depends on the extent of coordinate gene regulation. This review discusses the role of these glycosyltransferases in underpinning developmental and metabolic plasticity during adaptive responses.

Synthesis and biological activity of tetralone abscisic acid analogues

Bicyclic analogues of the plant hormone abscisic acid (ABA) were designed to incorporate the structural elements and functional groups of the parent molecule that are required for biological activity. The resulting tetralone analogues were predicted to have enhanced biological activity in plants, in part because oxidized products would not cyclize to forms corresponding to the inactive catabolite phaseic acid. The tetralone analogues were synthesized in seven steps from 1-tetralone and a range of analogues were accessible through a second route starting with 2-methyl-1-naphthol. Tetralone ABA 8 was found to have greater activity than ABA in two bioassays. The absolute configuration of (+)-8 was established by X-ray crystallography of a RAMP hydrazone derivative. The hydroxymethyl compounds 10 and 11, analogues for studying the roles of 8- and 9-hydroxy ABA 3 and 6, were also synthesized and found to be active.