ATP citrate lyase activity is post-translationally regulated by sink strength and impacts the wax, cutin and rubber biosynthetic pathways

An In Vitro Phytohormone Survey Reveals Concerted Regulation of the Cannabis Glandular Trichome Disc Cell Proteome

Cannabis (Cannabis sativa L.) flower glandular trichomes (GTs) are the main site of cannabinoid synthesis. Phytohormones, such as jasmonic acid (JA) and salicylic acid (SA), have been shown to increase cannabinoid content in cannabis flowers, but how this is regulated remains unknown. This study aimed to understand which biological processes in GT disc cells phytohormones control by using an in vitro assay. Live GT disc cells were isolated from a high-tetrahydrocannabinol cannabis cultivar and incubated on basal media plates supplemented with either kinetin (KIN), JA, SA, abscisic acid, ethephon, gibberellic acid, brassinolide, or sodium diethyldithiocarbamate. Quantitative proteomic analysis revealed that KIN, JA, and SA caused the greatest number of changes in the GT disc cell proteome. Surprisingly, none of the treatments concertedly increased cannabinoid content or the abundance of related biosynthetic proteins in the GT, suggesting that cannabinoid increases in previous in planta phytohormone studies are likely due to other processes, such as increased GT density. As well, KIN-, JA-, and SA-treated GTs had numerous differentially abundant proteins in common. Several were key proteins for leucoplast differentiation, cuticular wax and fatty acid metabolism, and primary metabolism regulation, denoting that cytokinin, JA, and SA signalling are likely important for coordinating cannabis GT differentiation and development.

Modulation of the Arabidopsis Starch Metabolic Network by the Cytosolic Acetyl-CoA Pathway in the Context of the Diurnal Illumination Cycle

The starch metabolic network was investigated in relation to other metabolic processes by examining a mutant with altered single-gene expression of ATP citrate lyase (ACL), an enzyme responsible for generating cytosolic acetyl-CoA pool from citrate. Previous research has shown that transgenic antisense plants with reduced ACL activity accumulate abnormally enlarged starch granules. In this study, we explored the underlying molecular mechanisms linking cytosolic acetyl-CoA generation and starch metabolism under short-day photoperiods. We performed transcriptome and quantification of starch accumulation in the leaves of wild-type and antisense seedlings with reduced ACL activity. The antisense-ACLA mutant accumulated more starch than the wild type under short-day conditions. Zymogram analyses were conducted to compare the activities of starch-metabolizing enzymes with transcriptomic changes in the seedling. Differential expression between wild-type and antisense-ACLA plants was detected in genes implicated in starch and acetyl-CoA metabolism, and cell wall metabolism. These analyses revealed a strong correlation between the transcript levels of genes responsible for starch synthesis and degradation, reflecting coordinated regulation at the transcriptomic level. Furthermore, our data provide novel insights into the regulatory links between cytosolic acetyl-CoA metabolism and starch metabolic pathways.

Multi-Omics Analyses of Lettuce (Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation

UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.

Plant terpenoid biosynthetic network and its multiple layers of regulation

Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.

Identification of CmACL genes in melon and analysis of their potential functions in fruit sugar and acid accumulation

Citric acid is the most important organic acid in melon and has a great influence on fruit flavor quality. ATP-citrate (pro-S) lyase (ACL) is a key regulator in the acetyl-CoA pathway and plays an important role in citric acid metabolism. In this study we analyzed the structure and phylogenetics of CmACL genes and their functions in sugar and acid accumulation in melon. A total of four CmACL genes were identified in the melon genome, and phylogenetic analysis assigned these genes into the α subfamily (CmACLα1 and CmACLα2) and the β subfamily (CmACLβ1 and CmACLβ2). Conserved motif and gene structure analyses showed that members of the same subfamily shared identical conserved motifs and gene structures, and probably have similar biological functions. Analysis of cis-acting elements revealed that CmACL promoter sequences contained regulatory elements related to light, stress, phytohormones, and growth and development, indicating that CmACL genes may be involved in melon growth and stress responses. The prediction of protein interaction network showed that CmACL proteins were closely related to the proteins belonging to tricarboxylic acid cycle, glyoxylic acid cycle and glycolytic pathway, suggesting that CmACL proteins may play an important role in sugar and acid metabolism. The expression of CmACLβ1 was significantly and positively correlated with sucrose content, and CmACLβ2 expression was significantly positively correlated with citric acid content, suggesting that CmACLβ1 and CmACLβ2 have important roles in sugar and acid accumulation in melon. Our results offer novel insights and avenues for the regulation of sugar and acid levels in melon and provide a theoretical foundation for breeding high-quality melon cultivars.

ABA spray on Arabidopsis seedlings increases mature plants vigor under optimal and water-deficit conditions partly by enhancing nitrogen assimilation

Here, we report the effects of a single abscisic acid (ABA) spray on Arabidopsis seedlings on growth, development, primary metabolism, and response to water-deficit stress in adult and next-generation plants. The experiments were performed over 2 years in two different laboratories in Iran and South Africa. In each experiment, fifty 7-day-old Arabidopsis seedlings were sprayed with 10 μM ABA, 1 mM H2 O2 , distilled water, or left without spraying as priming treatments. Water-deficit stress was applied on half of the plants in each treatment by withholding water 2 days after spraying. Results showed that a single ABA spray at the cotyledonary stage significantly increased plant biomass and delayed flowering. The ABA spray significantly enhanced drought tolerance so that the survival rate after rehydration was 100 and 33% in the first and the second experiments, respectively, for ABA-treated plants compared to 35 and 0% for water-sprayed plants. This enhanced drought tolerance was not inheritable. Metabolomics analyses suggested that ABA probably increases the antioxidant capacity of the plant cells and modulates tricarboxylic acid cycle toward enhanced nitrogen assimilation. Strikingly, we also observed that the early water spray decreases mature plant resilience under water-deficit conditions and cause substantial transient metabolomics perturbations.

Herbaceous peony PlACLB2 positively regulates red petal formation by promoting anthocyanin accumulation

ATP-citrate lyase (ACL) gene catalyzes the formation of acetyl-CoA to provide intermediate precursors for many secondary metabolites, and also plays an important role in anthocyanin biosynthesis of plants. Herbaceous peony (Paeonia lactiflora Pall.) is an international cut flower known for its rich flower colors, however, the function of the ACL gene in flower color regulation is still unclear. Here, double-colored P. lactiflora 'Hebao Jinlian' were used to study the molecular mechanism of red petal, and acetyl-CoA and anthocyanin biosynthesis related PlACLB2, PlCHS, PlDFR, PlANS, and PlbHLH1 genes were initially found to highly expressed in the red outer-petals. The expression pattern of PlACLB2 was consistent with the spatial accumulation of anthocyanins. The correlation analysis of PlACLB2 expression pattern, acetyl-CoA content, and anthocyanin accumulation revealed that PlACLB2 was positively correlated with the acetyl-CoA and anthocyanin contents with correlation coefficients of 0.82 and 0.80. Moreover, multiple sequence alignment identified two typical conserved domains in PlACLB2, and phylogenetic analysis clustered PlACLB2 into the ACLB clade. PlACLB2 was localized in the nucleus and cytoplasm. On the one hand, silencing PlACLB2 in P. lactiflora red outer-petal resulted in lighter petal color and decreased acetyl-CoA accumulation, and quantitative analysis detected that PlACLB2-silenced petals lost more anthocyanins than the control groups with a decrease of 31.0%, and the main pigment component cyanidin-3,5-O-diglucoside was reduced by 31.9%. On the other hand, overexpression of PlACLB2 significantly promoted red coloration, acetyl-CoA content, and anthocyanin accumulation in tobacco flowers. These results demonstrated that PlACLB2 promoted anthocyanin accumulation by increasing the abundance of its precursor substrate acetyl-CoA, thereby regulating the formation of the red petals in P. lactiflora.

Citric Acid-Mediated Abiotic Stress Tolerance in Plants

Several recent studies have shown that citric acid/citrate (CA) can confer abiotic stress tolerance to plants. Exogenous CA application leads to improved growth and yield in crop plants under various abiotic stress conditions. Improved physiological outcomes are associated with higher photosynthetic rates, reduced reactive oxygen species, and better osmoregulation. Application of CA also induces antioxidant defense systems, promotes increased chlorophyll content, and affects secondary metabolism to limit plant growth restrictions under stress. In particular, CA has a major impact on relieving heavy metal stress by promoting precipitation, chelation, and sequestration of metal ions. This review summarizes the mechanisms that mediate CA-regulated changes in plants, primarily CA’s involvement in the control of physiological and molecular processes in plants under abiotic stress conditions. We also review genetic engineering strategies for CA-mediated abiotic stress tolerance. Finally, we propose a model to explain how CA’s position in complex metabolic networks involving the biosynthesis of phytohormones, amino acids, signaling molecules, and other secondary metabolites could explain some of its abiotic stress-ameliorating properties. This review summarizes our current understanding of CA-mediated abiotic stress tolerance and highlights areas where additional research is needed.

Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity

Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.

Multiomic Analysis Elucidates the Reasons Underlying the Differential Metabolite Accumulation in Citrus Mature Leaves and Fruit Juice Sacs

Fruit and leaf possess distinctly different metabolites. Here, metabolites and transcriptome were compared between mature leaves (ML) and juice sacs (JS) of Citrus grandis "Hirado Buntan" to investigate the possible reasons. Results indicated that the remarkable difference in starch, total flavonoids and carotenoids, l-ascorbate, and jasmonic acid between ML and JS was tightly related to the expression levels of their biosynthesis-related genes, while the significant difference in abscisic acid and citrate was mainly related to the gene expression level(s) of 9-cis-epoxycarotenoid dioxygenase and proton pump genes, respectively. In addition, ATP citrate lyase probably plays a key role in the levels of flavonoids between ML and JS via providing different levels of acetyl-CoA. Taken together, these results identified some key candidate genes responsible for the content of a given metabolite and will contribute to research in regulating such metabolite content in citrus fruits.

Citrus CitERF6 Contributes to Citric Acid Degradation via Upregulation of CitAclα1, Encoding ATP-Citrate Lyase Subunit α

Citric acid is the most abundant organic acid in citrus fruit, and the acetyl-CoA pathway potentially plays an important role in citric acid degradation, which occurs during fruit ripening. Analysis of transcripts during fruit development of key genes in the acetyl-CoA pathway and transient overexpression assay in citrus leaves indicated that CitAclα1 could be a potential target gene involved in citrate degradation. In order to understand more about CitAclα1, 23 transcription factors coexpressed with CitAclα1 in citrus fruit were identified by RNA-seq. Using dual-luciferase assays, CitERF6 was shown to trans-activate the promoter of CitAclα1 and electrophoretic mobility shift assays (EMSAs) showed that CitERF6 directly bound to a 5'-CAACA-3' motif in the CitAclα1 promoter. Furthermore, citric acid content was significantly reduced when CitERF6 was overexpressed in transgenic tobacco leaves. Taken together, these results indicate an important role for CitERF6 in transcriptional regulation of CitAclα1 and control of citrate degradation.

PaACL silencing accelerates flower senescence and changes the proteome to maintain metabolic homeostasis in Petunia hybrida

Cytosolic acetyl-CoA is an intermediate of the synthesis of most secondary metabolites and the source of acetyl for protein acetylation. The formation of cytosolic acetyl-CoA from citrate is catalysed by ATP-citrate lyase (ACL). However, the function of ACL in global metabolite synthesis and global protein acetylation is not well known. Here, four genes, PaACLA1, PaACLA2, PaACLB1, and PaACLB2, which encode the ACLA and ACLB subunits of ACL in Petunia axillaris, were identified as the same sequences in Petunia hybrida 'Ultra'. Silencing of PaACLA1-A2 and PaACLB1-B2 led to abnormal leaf and flower development, reduced total anthocyanin content, and accelerated flower senescence in petunia 'Ultra'. Metabolome and acetylome analysis revealed that PaACLB1-B2 silencing increased the content of many downstream metabolites of acetyl-CoA metabolism and the levels of acetylation of many proteins in petunia corollas. Mechanistically, the metabolic stress induced by reduction of acetyl-CoA in PaACL-silenced petunia corollas caused global and specific changes in the transcriptome, the proteome, and the acetylome, with the effect of maintaining metabolic homeostasis. In addition, the global proteome and acetylome were negatively correlated under acetyl-CoA deficiency. Together, our results suggest that ACL acts as an important metabolic regulator that maintains metabolic homeostasis by promoting changes in the transcriptome, proteome. and acetylome.

Reconfiguring Plant Metabolism for Biodegradable Plastic Production

For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.

Comparative Metabolites and Citrate-Degrading Enzymes Activities in Citrus Fruits Reveal the Role of Balance between ACL and Cyt-ACO in Metabolite Conversions

Citric acid metabolism is considered to be the central cellular process of metabolite conversions. ATP-citrate lyase (ACL) and cytosolic aconitase (cyt-ACO) are the two citrate-degrading enzymes that decide the carbon flux towards different metabolite biosynthesis pathways. However, the correlation of their activities with metabolite concentrations in citrus fruits is still unclear. Here, the concentrations of soluble sugars, organic acids, acetyl-CoA, flavonoids, carotenoids, and γ-aminobutyric acid, as well as the activities of ACL, cyt-ACO, acetyl-CoA C-acetyltransferase, and acetyl-CoA carboxylase, were compared among the fruits of six citrus cultivars during fruit development and ripening. The results showed that the correlation between citrate concentration and cyt-ACO or ACL activity varied greatly among cultivars, while the activities of cyt-ACO and ACL had a significantly negative correlation (r = −0.4431). Moreover, ACL overexpression and RNA interference in the Citrus callus indicated that increasing and decreasing the ACL activity could reduce and induce cyt-ACO activity, respectively. In addition, significant correlation was only observed between the ACL activity and the concentration of acetyl-CoA (r = 0.4333). Taken together, the present study suggested that ACL and cyt-ACO synergistically control the citrate fate for the biosynthesis of other metabolites, but they are not the key determinants for the accumulation of citrate, as well as other metabolites in citrus fruits.

Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology

Taraxacum koksaghyz has been identified as one of the most promising alternative rubber crops. Its high-quality rubber is produced in the latex of laticifers, a specialized cell type that is organized in a network of elongated tubules throughout the entire plant body. In order to gain insights into the physiological role(s) of latex and hence laticifer biology, we examine the effects of barnase-induced latex RNA degradation on the metabolite and protein compositions in the roots. We established high-quality datasets that enabled precise discrimination between cellular and physiological processes in laticifers and non-laticifer cell types of roots at different vegetative stages. We identified numerous latex-specific proteins, including a perilipin-like protein that has not been studied in plants yet. The barnase-expressing plants revealed a phenotype that did not exude latex, which may provide a valuable genetic basis for future studies of plant-environment interactions concerning latex and also help to clarify the evolution and arbitrary distribution of latex throughout the plant kingdom. The overview of temporal changes in composition and protein abundance provided by our data opens the way for a deeper understanding of the molecular interactions, reactions, and network relationships that underlie the different metabolic pathways in the roots of this potential rubber crop.

Overexpression of HMG-CoA synthase promotes Arabidopsis root growth and adversely affects glucosinolate biosynthesis

3-Hydroxy-3-methylglutaryl-CoA synthase (HMGS) catalyses the second step of the mevalonate (MVA) pathway. An HMGS inhibitor (F-244) has been reported to retard growth in wheat, tobacco, and Brassica juncea, but the mechanism remains unknown. Although the effects of HMGS on downstream isoprenoid metabolites have been extensively reported, not much is known on how it might affect non-isoprenoid metabolic pathways. Here, the mechanism of F-244-mediated inhibition of primary root growth in Arabidopsis and the relationship between HMGS and non-isoprenoid metabolic pathways were investigated by untargeted SWATH-MS quantitative proteomics, quantitative real-time PCR, and target metabolite analysis. Our results revealed that the inhibition of primary root growth caused by F-244 was a consequence of reduced stigmasterol, auxin, and cytokinin levels. Interestingly, proteomic analyses identified a relationship between HMGS and glucosinolate biosynthesis. Inhibition of HMGS activated glucosinolate biosynthesis, resulting from the induction of glucosinolate biosynthesis-related genes, suppression of sterol biosynthesis-related genes, and reduction in sterol levels. In contrast, HMGS overexpression inhibited glucosinolate biosynthesis, due to down-regulation of glucosinolate biosynthesis-related genes, up-regulation of sterol biosynthesis-related genes, and increase in sterol content. Thus, HMGS might represent a target for the manipulation of glucosinolate biosynthesis, given the regulatory relationship between HMGS in the MVA pathway and glucosinolate biosynthesis.

Polyploidy remodels fruit metabolism by modifying carbon source utilization and metabolic flux in Ponkan mandarin (Citrus reticulata Blanco)

The phenotypic variations that follow polyploidization are expected to improve agricultural productivity and efficiency [1]. However, the effect of polyploidization on plant metabolism has rarely been studied. This study evaluated the metabolic alterations that followed autotetraploidization in the fruit of Ponkan mandarin (C. reticulata Blanco) for three consecutive years and explored the underlying changes to the transcriptome. The autotetraploid (4x) Ponkan fruit had higher levels of total acids, ascorbic acid and total phenolic compounds than the diploid (2x). The primary metabolites especially the organic acids tended to accumulate at higher levels in the 4x fruit. Conversely, two major groups of secondary metabolites (i.e. flavonoids and carotenoids) tended to accumulate at lower levels. The expression levels of citric acid biosynthesis-related genes were unaltered in 4x fruit compared to the 2x fruit. Additionally, genes associated with the transport and utilization of citric acid were significantly down-regulated during ripening, which might induce increases in the levels of citric acid in the 4x fruit. Lower levels of flavonoids and carotenoids in the 4x fruit are potentially associated with decreases in the transport and utilization of citric acid, which is an important metabolite. Citric acid contributes to respiration by serving as an intermediated in the tricarboxylic acid cycle (TCA) and also provides carbon for the production of secondary metabolites. This study demonstrates that polyploidization can influence metabolism in plants.

OsACL-A2 negatively regulates cell death and disease resistance in rice

ATP-citrate lyases (ACL) play critical roles in tumour cell propagation, foetal development and growth, and histone acetylation in human and animals. Here, we report a novel function of ACL in cell death-mediated pathogen defence responses in rice. Using ethyl methanesulphonate (EMS) mutagenesis and map-based cloning, we identified an Oryza sativa ACL-A2 mutant allele, termed spotted leaf 30-1 (spl30-1), in which an A-to-T transversion converts an Asn at position 343 to a Tyr (N343Y), causing a recessive mutation that led to a lesion mimic phenotype. Compared to wild-type plants, spl30-1 significantly reduces ACL enzymatic activity, accumulates high reactive oxygen species and increases degradation rate of nuclear deoxyribonucleic acids. CRISPR/Cas9-mediated insertion/deletion mutation analysis and complementation assay confirmed that the phenotype of spl30-1 resulted from the defective function of OsACL-A2 protein. We further biochemically identified that the N343Y mutation caused a significant degradation of SPL30^N343Y in a ubiquitin-26S proteasome system (UPS)-dependent manner without alteration in transcripts of OsACL-A2 in spl30-1. Transcriptome analysis identified a number of up-regulated genes associated with pathogen defence responses in recessive mutants of OsACL-A2, implying its role in innate immunity. Suppressor mutant screen suggested that OsSL, which encodes a P450 monooxygenase protein, acted as a downstream key regulator in spl30-1-mediated pathogen defence responses. Taken together, our study discovered a novel role of OsACL-A2 in negatively regulating innate immune responses in rice.

Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica

Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.

The Cuticle Mutant eca2 Modifies Plant Defense Responses to Biotrophic and Necrotrophic Pathogens and Herbivory Insects

We isolated previously several Arabidopsis thaliana mutants with constitutive expression of the early microbe-associated molecular pattern-induced gene ATL2, named eca (expresión constitutiva de ATL2). Here, we further explored the interaction of eca mutants with pest and pathogens. Of all eca mutants, eca2 was more resistant to a fungal pathogen (Botrytis cinerea) and a bacterial pathogen (Pseudomonas syringae) as well as to a generalist herbivorous insect (Spodoptera littoralis). Permeability of the cuticle is increased in eca2; chemical characterization shows that eca2 has a significant reduction of both cuticular wax and cutin. Additionally, we determined that eca2 did not display a similar compensatory transcriptional response, compared with a previously characterized cuticular mutant, and that resistance to B. cinerea is mediated by the priming of the early and late induced defense responses, including salicylic acid- and jasmonic acid-induced genes. These results suggest that ECA2-dependent responses are involved in the nonhost defense mechanism against biotrophic and necrotrophic pathogens and against a generalist insect by modulation and priming of innate immunity and late defense responses. Making eca2 an interesting model to characterize the molecular basis for plant defenses against different biotic interactions and to study the initial events that take place in the cuticle surface of the aerial organs.

Development of rubber-enriched dandelion varieties by metabolic engineering of the inulin pathway

Natural rubber (NR) is an important raw material for a large number of industrial products. The primary source of NR is the rubber tree Hevea brasiliensis, but increased worldwide demand means that alternative sustainable sources are urgently required. The Russian dandelion (Taraxacum koksaghyz Rodin) is such an alternative because large amounts of NR are produced in its root system. However, rubber biosynthesis must be improved to develop T. koksaghyz into a commercially feasible crop. In addition to NR, T. koksaghyz also produces large amounts of the reserve carbohydrate inulin, which is stored in parenchymal root cell vacuoles near the phloem, adjacent to apoplastically separated laticifers. In contrast to NR, which accumulates throughout the year even during dormancy, inulin is synthesized during the summer and is degraded from the autumn onwards when root tissues undergo a sink-to-source transition. We carried out a comprehensive analysis of inulin and NR metabolism in T. koksaghyz and its close relative T. brevicorniculatum and functionally characterized the key enzyme fructan 1-exohydrolase (1-FEH), which catalyses the degradation of inulin to fructose and sucrose. The constitutive overexpression of Tk1-FEH almost doubled the rubber content in the roots of two dandelion species without any trade-offs in terms of plant fitness. To our knowledge, this is the first study showing that energy supplied by the reserve carbohydrate inulin can be used to promote the synthesis of NR in dandelions, providing a basis for the breeding of rubber-enriched varieties for industrial rubber production.

Isoprenoid biosynthesis in dandelion latex is enhanced by the overexpression of three key enzymes involved in the mevalonate pathway

BACKGROUND

Latex from the dandelion species Taraxacum brevicorniculatum contains many high-value isoprenoid end products, e.g. triterpenes and polyisoprenes such as natural rubber. The isopentenyl pyrophosphate units required as precursors for these isoprenoids are provided by the mevalonate (MVA) pathway. The key enzyme in this pathway is 3-hydroxy-methyl-glutaryl-CoA reductase (HMGR) and its activity has been thoroughly characterized in many plant species including dandelion. However, two enzymes acting upstream of HMGR have not been characterized in dandelion latex: ATP citrate lyase (ACL), which provides the acetyl-CoA utilized in the MVA pathway, and acetoacetyl-CoA thiolase (AACT), which catalyzes the first step in the pathway to produce acetoacetyl-CoA. Here we isolated ACL and AACT genes from T. brevicorniculatum latex and characterized their expression profiles. We also overexpressed the well-characterized HMGR, ACL and AACT genes from Arabidopsis thaliana in T. brevicorniculatum to determine their impact on isoprenoid end products in the latex.

RESULTS

The spatial and temporal expression profiles of T. brevicorniculatum ACL and AACT revealed their pivotal role in the synthesis of precursors necessary for isoprenoid biosynthesis in latex. The overexpression of A. thaliana ACL and AACT and HMGR in T. brevicorniculatum latex resulted in the accumulation of all three enzymes, increased the corresponding enzymatic activities and ultimately increased sterol levels by ~5-fold and pentacyclic triterpene and cis-1,4-isoprene levels by ~2-fold. Remarkably high levels of the triterpene precursor squalene were also detected in the triple-transgenic lines (up to 32 mg/g root dry weight) leading to the formation of numerous lipid droplets which were observed in root cross-sections.

CONCLUSIONS

We could show the effective expression of up to three transgenes in T. brevicorniculatum latex which led to increased enzymatic activity and resulted in high level squalene accumulation in the dandelion roots up to an industrially relevant amount. Our data provide insight into the regulation of the MVA pathway in dandelion latex and can be used as a basis for metabolic engineering to enhance the production of isoprenoid end products in this specialized tissue.

Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves

BACKGROUND

Conventional metabolomics approaches face the problem of hidden metabolic phenotypes where only fluxes are altered but pool sizes stay constant. Metabolic flux experiments are used to detect such hidden flux phenotypes. These experiments are, however, time consuming, may be cost intensive, and involve specialists for modeling. We fill the gap between conventional metabolomics and flux modeling. We present rapid stable isotope tracing assays and analysis strategies of ¹³C labeling data. For this purpose, we combine the conventional metabolomics approach that detects significant relative changes of metabolite pool sizes with analyses of differential utilization of ¹³C labeled carbon. As a test case, we use uniformly labeled ¹³C-sucrose.

RESULTS

We present petiole and hypocotyl feeding assays for the rapid in situ feeding (≤ 4 h) of isotopically labeled metabolic precursor to whole Arabidopsis thaliana rosettes. The assays are assessed by conventional gas chromatography-mass spectrometry based metabolite profiling that was extended by joined differential analysis of ¹³C-labeled sub-pools and of ¹³C enrichment of metabolites relative to the enrichment of ¹³C-sucrose within each sample. We apply these analyses to the sink to source transition continuum of leaves from single A. thaliana rosettes and characterize the associated relative changes of metabolite pools, as well as previously hidden changes of sucrose-derived carbon partitioning. We compared the contribution of sucrose as a carbon source in predominantly sink to predominantly source leaves and identified a set of primary metabolites with differential carbon utilization during sink to source transition.

CONCLUSION

The presented feeding assays and data evaluation strategies represent a rapid and easy-to-use tool box for enhanced metabolomics studies that combine differential pool size analysis with screening for differential carbon utilization from defined stable isotope labeled metabolic precursors.

Citrate Accumulation-Related Gene Expression and/or Enzyme Activity Analysis Combined With Metabolomics Provide a Novel Insight for an Orange Mutant

'Hong Anliu' (HAL, Citrus sinensis cv. Hong Anliu) is a bud mutant of 'Anliu' (AL), characterized by a comprehensive metabolite alteration, such as lower accumulation of citrate, high accumulation of lycopene and soluble sugars in fruit juice sacs. Due to carboxylic acid metabolism connects other metabolite biosynthesis and/or catabolism networks, we therefore focused analyzing citrate accumulation-related gene expression profiles and/or enzyme activities, along with metabolic fingerprinting between 'HAL' and 'AL'. Compared with 'AL', the transcript levels of citrate biosynthesis- and utilization-related genes and/or the activities of their respective enzymes such as citrate synthase, cytosol aconitase and ATP-citrate lyase were significantly higher in 'HAL'. Nevertheless, the mitochondrial aconitase activity, the gene transcript levels of proton pumps, including vacuolar H(+)-ATPase, vacuolar H(+)-PPase, and the juice sac-predominant p-type proton pump gene (CsPH8) were significantly lower in 'HAL'. These results implied that 'HAL' has higher abilities for citrate biosynthesis and utilization, but lower ability for the citrate uptake into vacuole compared with 'AL'. Combined with the metabolites-analyzing results, a model was then established and suggested that the reduction in proton pump activity is the key factor for the low citrate accumulation and the comprehensive metabolite alterations as well in 'HAL'.

Peculiarities and impacts of expression of bacterial cyanophycin synthetases in plants

Cyanophycin (CP) can be successfully produced in plants by the ectopic expression of the CphA synthetase from Thermosynechococcus elongatus BP-1 (Berg et al. 2000), yielding up to 6.8 % of dry weight (DW) in tobacco leaf tissue and 7.5 % in potato tubers (Huehns et al. 2008, 2009). Though, high amounts of the polymer lead to phenotypical abnormalities in both crops. The extension of abnormalities and the maximum amount of CP tolerated depend on the compartment that CP production is localized at the tissue/crop in which CP was produced (Huehns et al. 2008, 2009; Neumann et al. 2005). It cannot be ascribed to a depletion of arginine, lysine, or aspartate, the substrates for CP synthesis.

Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses

The epidermis on leaves protects plants from pathogen invasion and provides a waterproof barrier. It consists of a layer of cells that is surrounded by thick cell walls, which are partially impregnated by highly hydrophobic cuticular components. We show that the Arabidopsis T-DNA insertion mutants of REDUCED WALL ACETYLATION 2 (rwa2), previously identified as having reduced O-acetylation of both pectins and hemicelluloses, exhibit pleiotrophic phenotype on the leaf surface. The cuticle layer appeared diffused and was significantly thicker and underneath cell wall layer was interspersed with electron-dense deposits. A large number of trichomes were collapsed and surface permeability of the leaves was enhanced in rwa2 as compared to the wild type. A massive reprogramming of the transcriptome was observed in rwa2 as compared to the wild type, including a coordinated up-regulation of genes involved in responses to abiotic stress, particularly detoxification of reactive oxygen species and defense against microbial pathogens (e.g., lipid transfer proteins, peroxidases). In accordance, peroxidase activities were found to be elevated in rwa2 as compared to the wild type. These results indicate that cell wall acetylation is essential for maintaining the structural integrity of leaf epidermis, and that reduction of cell wall acetylation leads to global stress responses in Arabidopsis.

Thioredoxin, a master regulator of the tricarboxylic acid cycle in plant mitochondria

Plant mitochondria have a fully operational tricarboxylic acid (TCA) cycle that plays a central role in generating ATP and providing carbon skeletons for a range of biosynthetic processes in both heterotrophic and photosynthetic tissues. The cycle enzyme-encoding genes have been well characterized in terms of transcriptional and effector-mediated regulation and have also been subjected to reverse genetic analysis. However, despite this wealth of attention, a central question remains unanswered: "What regulates flux through this pathway in vivo?" Previous proteomic experiments with Arabidopsis discussed below have revealed that a number of mitochondrial enzymes, including members of the TCA cycle and affiliated pathways, harbor thioredoxin (TRX)-binding sites and are potentially redox-regulated. We have followed up on this possibility and found TRX to be a redox-sensitive mediator of TCA cycle flux. In this investigation, we first characterized, at the enzyme and metabolite levels, mutants of the mitochondrial TRX pathway in Arabidopsis: the NADP-TRX reductase a and b double mutant (ntra ntrb) and the mitochondrially located thioredoxin o1 (trxo1) mutant. These studies were followed by a comparative evaluation of the redistribution of isotopes when (13)C-glucose, (13)C-malate, or (13)C-pyruvate was provided as a substrate to leaves of mutant or WT plants. In a complementary approach, we evaluated the in vitro activities of a range of TCA cycle and associated enzymes under varying redox states. The combined dataset suggests that TRX may deactivate both mitochondrial succinate dehydrogenase and fumarase and activate the cytosolic ATP-citrate lyase in vivo, acting as a direct regulator of carbon flow through the TCA cycle and providing a mechanism for the coordination of cellular function.

The global regulator FfSge1 is required for expression of secondary metabolite gene clusters but not for pathogenicity in Fusarium fujikuroi

The plant pathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce several other secondary metabolites (SMs). Although much progress has been made in the field of secondary metabolism, the transcriptional regulation of SM biosynthesis is complex and still incompletely understood. Environmental conditions, global as well as pathway-specific regulators and chromatin remodelling have been shown to play major roles. Here, the role of FfSge1, a homologue of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for formation of conidia and pathogenicity but is involved in vegetative growth. Transcriptome analysis of the mutant Δffsge1 compared with the wild type, as well as comparative chemical analysis between the wild type, Δffsge1 and OE:FfSGE1, revealed that FfSge1 functions as a global activator of secondary metabolism in F. fujikuroi. Double mutants of FfSGE1 and other SM regulatory genes brought insights into the hierarchical regulation of secondary metabolism. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a non-canonical non-ribosomal peptide synthetase.

Genome-wide identification of citrus ATP-citrate lyase genes and their transcript analysis in fruits reveals their possible role in citrate utilization

ATP-citrate lyase (ACL, EC4.1.3.8) catalyzes citrate to oxaloacetate and acetyl-CoA in the cell cytosol, and has important roles in normal plant growth and in the biosynthesis of some secondary metabolites. We identified three ACL genes, CitACLα1, CitACLα2, and CitACLβ1, in the citrus genome database. Both CitACLα1 and CitACLα2 encode putative ACL α subunits with 82.5 % amino acid identity, whereas CitACLβ1 encodes a putative ACL β subunit. Gene structure analysis showed that CitACLα1 and CitACLα2 had 12 exons and 11 introns, and CitACLβ1 had 16 exons and 15 introns. CitACLα1 and CitACLβ1 were predominantly expressed in flower, and CitACLα2 was predominantly expressed in stem and fibrous roots. As fruits ripen, the transcript levels of CitACLα1, CitACLβ1, and/or CitACLα2 in cultivars 'Niuher' and 'Owari' increased, accompanied by significant decreases in citrate content, while their transcript levels decreased significantly in 'Egan No. 1' and 'Iyokan', although citrate content also decreased. In 'HB pummelo', in which acid content increased as fruit ripened, and in acid-free pummelo, transcript levels of CitACLα2, CitACLβ1, and/or CitACLα1 increased. Moreover, mild drought stress and ABA treatment significantly increased citrate contents in fruits. Transcript levels of the three genes were significantly reduced by mild drought stress, and the transcript level of only CitACLβ1 was significantly reduced by ABA treatment. Taken together, these data indicate that the effects of ACL on citrate use during fruit ripening depends on the cultivar, and the reduction in ACL gene expression may be attributed to citrate increases under mild drought stress or ABA treatment.