Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases

Phenotypic diploidization in plant functional traits uncovered by synthetic neopolyploids in Dianthus broteri

Whole-genome duplication and post-polyploidization genome downsizing play key roles in the evolution of land plants; however, the impact of genomic diploidization on functional traits still remains poorly understood. Using Dianthus broteri as a model, we compared the ecophysiological behaviour of colchicine-induced neotetraploids (4xNeo) to diploids (2x) and naturally occurring tetraploids (4xNat). Leaf gas-exchange and chlorophyll fluorescence analyses were performed in order to asses to what extent post-polyploidization evolutionary processes have affected 4xNat. Genomic diploidization and phenotypic novelty were evident. Distinct patterns of variation revealed that post-polyploidization processes altered the phenotypic shifts directly mediated by genome doubling. The photosynthetic phenotype was affected in several ways but the main effect was phenotypic diploidization (i.e. 2x and 4xNat were closer to each other than to 4xNeo). Overall, our results show the potential benefits of considering experimentally synthetized versus naturally established polyploids when exploring the role of polyploidization in promoting functional divergence.

Three-in-One Simultaneous Extraction of Proteins, Metabolites and Lipids for Multi-Omics

Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics, and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical properties. Therefore, several sets/aliquots of samples are needed for extracting different molecules. Here we adapted a biphasic fractionation method to extract proteins, metabolites, and lipids from the same sample (3-in-1) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) multi-omics. To demonstrate utility of the improved method, we used bacteria-primed Arabidopsis leaves to generate multi-omics datasets from the same sample. In total, we were able to analyze 1849 proteins, 1967 metabolites, and 424 lipid species in single samples. The molecules cover a wide range of biological and molecular processes, and allow quantitative analyses of different molecules and pathways. Our results have shown the clear advantages of the multi-omics method, including sample conservation, high reproducibility, and tight correlation between different types of biomolecules.

Metabolic response of bok choy leaves under chromium pollution stress

Chromium (Cr) pollution in farmlands is a common environmental issue, that can seriously inhibit plant growth, damage plant cells, and even cause plant death. In this study, bok choy (Brassica campestris L. ssp. chinensis Makino (var. communis Tsen et Lee)) was selected as a model plant to investigate the metabolic response to Cr stress at concentrations of 2.0 mg/L and 8.0 mg/L. Metabolites were identified using gas chromatography-mass spectrometry. Principal component analysis and orthogonal projections to latent structure discriminant analysis revealed the notable effect of Cr stress on the metabolites of bok choy. Under Cr stress, 145 metabolites were identified in the bok choy leaves. At 2.0 mg/L Cr stress, 10 and 26 metabolites changed compared to the control after 7 d and 14 d, respectively. At 8.0 mg/L Cr stress, 24 and 24 metabolites changed significantly after 7 and 14 d, respectively. The data showed that metabolism was affected by the Cr stress concentration and exposure time. Specifically, under the Cr stress, the tricarboxylic acid cycle, glutamine synthetase/glutamate synthase cycle, and partial amino acid metabolic pathways were blocked, inhibiting the normal growth and development of bok choy. The change of citric acid content was the most significant, and the accumulation of citric acid indicated the degree of plant Cr toxicity and resistance. These results would facilitate further dissection of the mechanisms of heavy metal accumulation/tolerance in plants and the effective management of such contamination in vegetable crops by genetic manipulation.

Protein complex formation in methionine chain-elongation and leucine biosynthesis

During the past two decades, glucosinolate (GLS) metabolic pathways have been under extensive studies because of the importance of the specialized metabolites in plant defense against herbivores and pathogens. The studies have led to a nearly complete characterization of biosynthetic genes in the reference plant Arabidopsis thaliana. Before methionine incorporation into the core structure of aliphatic GLS, it undergoes chain-elongation through an iterative three-step process recruited from leucine biosynthesis. Although enzymes catalyzing each step of the reaction have been characterized, the regulatory mode is largely unknown. In this study, using three independent approaches, yeast two-hybrid (Y2H), coimmunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC), we uncovered the presence of protein complexes consisting of isopropylmalate isomerase (IPMI) and isopropylmalate dehydrogenase (IPMDH). In addition, simultaneous decreases in both IPMI and IPMDH activities in a leuc:ipmdh1 double mutants resulted in aggregated changes of GLS profiles compared to either leuc or ipmdh1 single mutants. Although the biological importance of the formation of IPMI and IPMDH protein complexes has not been documented in any organisms, these complexes may represent a new regulatory mechanism of substrate channeling in GLS and/or leucine biosynthesis. Since genes encoding the two enzymes are widely distributed in eukaryotic and prokaryotic genomes, such complexes may have universal significance in the regulation of leucine biosynthesis.

Protective role of nitric oxide on nitrogen-thiol metabolism and amino acids profiling during arsenic exposure in Oryza sativa L

Nitric oxide (NO) being a signaling molecule inside the plant cells, play significant role in signaling cascades and protection against environmental stresses. However, the protective role of NO in alleviating As toxicity in rice plants is currently not available. In the present study, the level of NO, nitrogen (N), inorganic N (nitrate, ammonium), thiols {TT (Total thiols), NPT (Nonprotein thiol)} and AAs contents along with N assimilating enzymes (NR, GDH, GOGAT) were analyzed after exposure of As^III/NO treatment alone, and in combination. NO supplementation enhanced the content of N, inorganic N & thiol contents, NR, GOGAT activities, when compared with As^III exposure alone. In As^III exposed rice seedlings, content of AAs (except His, Arg, Met) reduced over the control, while supplementation of SNP improved AAs contents, compared to As^III treatment alone. In conclusion, rice seedlings supplemented with NO tolerate the As^III toxicity by reducing the N related parameters, thiol contents, altering the AA profile and enhanced the nutritional quality by increasing EAAs (essential amino acids) and NEAAs (non-essential amino acids).

The role and proteomic analysis of ethylene in hydrogen gas-induced adventitious rooting development in cucumber (Cucumis sativus L.) explants

Previous studies have shown that both hydrogen gas (H₂) and ethylene (ETH) play positive roles in plant adventitious rooting. However, the relationship between H₂and ETH during this process has not been explored and remains insufficiently understood. In this study, cucumber (Cucumis sativus L.) was used to explore the proteomic changes in ETH-H₂-induced rooting. Our results show that hydrogen-rich water (HRW) and ethylene-releasing compound (ethephon) at proper concentrations promote adventitious rooting, with maximal biological responses occurring at 50% HRW or 0.5 µM ethephon. ETH inhibitors aminoethoxyvinylglycine (AVG) and AgNO₃ cause partial inhibition of adventitious rooting induced by H₂, suggesting that ETH might be involved in H₂-induced adventitious rooting. According to two-dimensional electrophoresis (2-DE) and mass spectrometric analyses, compared with the control, 9 proteins were up-regulated while 15 proteins were down-regulated in HRW treatment; four proteins were up-regulated while 10 proteins were down-regulated in ethephon treatment; and one protein was up-regulated while nine proteins were down-regulated in HRW+AVG treatment. Six of these differentially accumulated proteins were further analyzed, including photosynthesis -related proteins (ribulose-1,5-bisphosphate carall boxylase smsubunit (Rubisco), sedoheptulose-1,7-bisphosphatase (SBPase), oxygen-evolving enhancer protein (OEE1)), amino and metabolism-related protein (threonine dehydratase (TDH)), stress response-related protein (cytosolic ascorbate peroxidase (CAPX)), and folding, modification and degradation-related protein (protein disulfide-isomerase (PDI)). Moreover, the results of real-time PCR about the mRNA levels of these genes in various treatments were consistent with the 2-DE results. Therefore, ETH may be the downstream signaling molecule during H₂- induced adventitious rooting and proteins Rubisco, SBPase, OEE1, TDH, CAPX and PDI may play important roles during the process.

Biotechnological approaches in glucosinolate production

Glucosinolates (GLSs) are sulfur-rich, amino acid-derived defense compounds characteristic of the Brassicales order. In the past, GLSs were mostly known as anti-nutritional factors in fodder, biopesticides in agriculture, and flavors in condiments such as mustard. However, in recent times, GLSs have received increased attention as promoters of human health. This has spurred intensive research towards generating rich sources of health-promoting GLSs. We provide a comprehensive overview of the biotechnological approaches applied to reach this goal. This includes optimization of GLS production and composition in native, GLS-producing plants, including hairy root and cell cultures thereof, as well as synthetic biology approaches in heterologous hosts, such as tobacco and the microbial organisms Escherichia coli and Saccharomyces cerevisiae. The progress using these different approaches is discussed.

Effects of cadmium stress on growth and amino acid metabolism in two Compositae plants

Cadmium, a high toxic heavy metal, is one of the most serious contaminants in soil and a potential threat to plant growth and human health. Amino acid metabolism has the central role in heavy metal stress resistance of plants. In this paper, a pot experiment was carried out to study the effects of different concentrations of cadmium (0, 3, 6, 12, 30 mg kg^-1) on the growth, Cd accumulation and amino acid metabolism in two Compositae plants (Ageratum conyzoides L. and Crassocephalum crepidioides). The results showed that under cadmium stress, C. crepidioides accumulated more Cd in its shoot and was tolerant to Cd, whereas its low Cd-accumulating relative, A. conyzoides, suffered reduced growth. The Cd content in the aerial part of C. crepidioides exceeded the threshold of Cd-hyperaccumulator. Furthermore, the bioaccumulation factor (BCF) and biological transfer factor (BTF) values for Cd in C. crepidioides were > 1. Thus, C. crepidioides can be regarded as Cd-hyperaccumulator. The comparison between both studied plants indicated that Cd stress resulted in a differential but coordinated response of amino acid levels, which are playing a significant role in plant adaptation to Cd stress. Glu, Gln, Asp, Asn, Gaba, Val and Ala dominated the major amino acids. Higher Cd tolerance and Cd accumulation in C. crepidioides was associated with greater accumulation of free amino acids, especially for Gln and Asn, in C. crepidioides than in A. conyzoides.

Proteomics and Phosphoproteomics of Heat Stress-Responsive Mechanisms in Spinach

Elevated temperatures limit plant growth and reproduction and pose a growing threat to agriculture. Plant heat stress response is highly conserved and fine-tuned in multiple pathways. Spinach (Spinacia oleracea L.) is a cold tolerant but heat sensitive green leafy vegetable. In this study, heat adaptation mechanisms in a spinach sibling inbred heat-tolerant line Sp75 were investigated using physiological, proteomic, and phosphoproteomic approaches. The abundance patterns of 911 heat stress-responsive proteins, and phosphorylation level changes of 45 phosphoproteins indicated heat-induced calcium-mediated signaling, ROS homeostasis, endomembrane trafficking, and cross-membrane transport pathways, as well as more than 15 transcription regulation factors. Although photosynthesis was inhibited, diverse primary and secondary metabolic pathways were employed for defense against heat stress, such as glycolysis, pentose phosphate pathway, amino acid metabolism, fatty acid metabolism, nucleotide metabolism, vitamin metabolism, and isoprenoid biosynthesis. These data constitute a heat stress-responsive metabolic atlas in spinach, which will springboard further investigations into the sophisticated molecular mechanisms of plant heat adaptation and inform spinach molecular breeding initiatives.

Cadmium toxicity induced contrasting patterns of concentrations of free sarcosine, specific amino acids and selected microelements in two Noccaea species

Cadmium (Cd) toxicity affects numerous metabolic processes in plants. In the presence of Cd, plants accumulate specific amino acids which may be beneficial to developing Cd tolerance. Our study aimed to characterize the changes in the metabolism of selected free amino acids that are associated with Cd tolerance, and investigate the levels of selected microelements in order to relate these changes to the adaptation strategies of two metallophytes-Noccaea caerulescens (Redlschlag, Austria) and Noccaea praecox (Mežica, Slovenia). The plants were exposed to Cd contamination (90 mg Cd/kg soil) for 120 days in a pot experiment. Our results showed higher Cd accumulation in N. praecox compared to N. caerulescens. Cadmium contamination reduced the zinc and nickel levels in both species and a mixed effect was determined for copper and manganese content. Differences in free amino acid metabolism were observed between the two metallophytes growing under Cd-free and Cd-loaded conditions. Under Cd-free conditions, aromatic amino acids (phenylalanine, tryptophan and tyrosine) and branched-chain amino acids (leucine, isoleucine and valine) were accumulated more in the leaves of N. praecox than in N. caerulescens. Cd stress increased the content of these amino acids in both species but this increase was significant only in N. caerulescens leaves. Marked differences in the responses of the two species to Cd stress were shown for alanine, phenylalanine, threonine and sarcosine. Cadmium contamination also induced an increase of threonine as alanine and sarcosine decrease, which was larger in N. caerulescens than in N. praecox. All these factors contribute to the higher adaptation of N. praecox to Cd stress.

Combined Metabolomics and Proteomics Analysis of Major Depression in an Animal Model: Perturbed Energy Metabolism in the Chronic Mild Stressed Rat Cerebellum

Major depressive disorder (MDD) is a highly prevalent, debilitating mental illness of importance for global health. However, its molecular pathophysiology remains poorly understood. Combined proteomics and metabolomics approaches should provide a comprehensive understanding of MDD's etiology. The present study reports novel "-omics" insights from a rodent model of MDD. Cerebellar samples from chronic mild stressed (CMS)-treated depressed rats and controls were compared with a focus on the differentially expressed proteins and metabolites using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics and gas chromotography/mass spectrometry (GC-MS) metabolomics techniques, respectively. The combined analyses found significant alterations associated with cerebellar energy metabolism, as indicated by (1) abnormal amino acid metabolism accompanied by corresponding metabolic enzymatic alterations and disturbed protein turnover, (2) increased glycolytic and tricarboxylic acid (TCA) cycle enzyme levels paralleled by changes in the concentrations of associated metabolites, and (3) perturbation of ATP biosynthesis through adenosine accompanied by perturbation of the mitochondrial respiratory chain. To the best of our knowledge, this study is the first to integrate proteomics and metabolomics analyses to examine the pathophysiological mechanism(s) underlying MDD in a CMS rodent model of depression. These results can offer important insights into the pathogenesis of MDD.

Optimization of Engineered Production of the Glucoraphanin Precursor Dihomomethionine in Nicotiana benthamiana

Glucosinolates are natural products characteristic of the Brassicales order, which include vegetables such as cabbages and the model plant Arabidopsis thaliana. Glucoraphanin is the major glucosinolate in broccoli and associated with the health-promoting effects of broccoli consumption. Toward our goal of creating a rich source of glucoraphanin for dietary supplements, we have previously reported the feasibility of engineering glucoraphanin in Nicotiana benthamiana through transient expression of glucoraphanin biosynthetic genes from A. thaliana (Mikkelsen et al., 2010). As side-products, we obtained fivefold to eightfold higher levels of chain-elongated leucine-derived glucosinolates, not found in the native plant. Here, we investigated two different strategies to improve engineering of the methionine chain elongation part of the glucoraphanin pathway in N. benthamiana: (1) coexpression of the large subunit (LSU1) of the heterodimeric isopropylmalate isomerase and (2) coexpression of BAT5 transporter for efficient transfer of intermediates across the chloroplast membrane. We succeeded in raising dihomomethionine (DHM) levels to a maximum of 432 nmol g⁻¹ fresh weight that is equivalent to a ninefold increase compared to the highest production of this intermediate, as previously reported (Mikkelsen et al., 2010). The increased DHM production without increasing leucine-derived side-product levels provides new metabolic engineering strategies for improved glucoraphanin production in a heterologous host.

Physiological differences in response to di-n-butyl phthalate (DBP) exposure between low- and high-DBP accumulating cultivars of Chinese flowering cabbage (Brassica parachinensis L.)

To increase understanding on the mechanisms of cultivar difference in contaminant accumulation in crops, this study was designed to compare the physiological responses to di-n-butyl phthalate (DBP) exposure between low (Lvbao70) and high (Huaguan) DBP cultivars of Chinese flowering cabbage (Brassica parachinensis L.). Under high DBP exposure, significant differences in various physiological responses were observed between the two cultivars, which might account for the variation in DBP accumulation. Ultrastructure observation also showed different alterations or damages in the mesophyll cell structures between both cultivars, especially for the chloroplast disintegration, starch grain quantity, and plastoglobuli accumulation. Compared with Huaguan, Lvbao70 suffered greater decreases in biomass, chlorophyll content, carbon assimilation, gas exchange parameters, photosynthetic electron transport capacity, and antioxidase activities, which would have resulted in a great reduction of photosynthetic capacity. Although Lvbao70 enhanced energy dissipation and activities of some antioxidant enzymes, they did not provide sufficient protection against oxidative damage caused by DBP. The result suggested that the lower DBP tolerance of Lvbao70 might be associated with its poor physiological performances, which was responsible for its lower DBP accumulation to protect itself from toxicity. Additionally, Lvbao70 had a significantly lower transpiration rate and stomatal conductance than Huaguan, which might be the factors regulating DBP-accumulation variation.

Proteomic analysis of amino acid metabolism differences between wild and cultivated Panax ginseng

Background

The present study aimed to compare the relative abundance of proteins and amino acid metabolites to explore the mechanisms underlying the difference between wild and cultivated ginseng (Panax ginseng Meyer) at the amino acid level.

Methods

Two-dimensional polyacrylamide gel electrophoresis and isobaric tags for relative and absolute quantitation were used to identify the differential abundance of proteins between wild and cultivated ginseng. Total amino acids in wild and cultivated ginseng were compared using an automated amino acid analyzer. The activities of amino acid metabolism-related enzymes and the contents of intermediate metabolites between wild and cultivated ginseng were measured using enzyme-linked immunosorbent assay and spectrophotometric methods.

Results

Our results showed that the contents of 14 types of amino acids were higher in wild ginseng compared with cultivated ginseng. The amino acid metabolism-related enzymes and their derivatives, such as glutamate decarboxylase and S-adenosylmethionine, all had high levels of accumulation in wild ginseng. The accumulation of sulfur amino acid synthesis-related proteins, such as methionine synthase, was also higher in wild ginseng. In addition, glycolysis and tricarboxylic acid cycle-related enzymes as well as their intermediates had high levels of accumulation in wild ginseng.

Conclusion

This study elucidates the differences in amino acids between wild and cultivated ginseng. These results will provide a reference for further studies on the medicinal functions of wild ginseng.

Thiol-based redox proteins in abscisic acid and methyl jasmonate signaling in Brassica napus guard cells

Reversibly oxidized cysteine sulfhydryl groups serve as redox sensors or targets of redox sensing that are important in various physiological processes. However, little is known about redox-sensitive proteins in guard cells and how they function in stomatal signaling. In this study, Brassica napus guard-cell proteins altered by redox in response to abscisic acid (ABA) or methyl jasmonate (MeJA) were identified by complementary proteomics approaches, saturation differential in-gel electrophoresis and isotope-coded affinity tagging. In total, 65 and 118 potential redox-responsive proteins were identified in ABA- and MeJA-treated guard cells, respectively. All the proteins contain at least one cysteine, and over half of them are predicted to form intra-molecular disulfide bonds. Most of the proteins fall into the functional groups of 'energy', 'stress and defense' and 'metabolism'. Based on the peptide sequences identified by mass spectrometry, 30 proteins were common to ABA- and MeJA-treated samples. A total of 44 cysteines were mapped in the identified proteins, and their levels of redox sensitivity were quantified. Two of the proteins, a sucrose non-fermenting 1-related protein kinase and an isopropylmalate dehydrogenase, were confirmed to be redox-regulated and involved in stomatal movement. This study creates an inventory of potential redox switches, and highlights a protein redox regulatory mechanism in ABA and MeJA signal transduction in guard cells.

The small subunit 1 of the Arabidopsis isopropylmalate isomerase is required for normal growth and development and the early stages of glucosinolate formation

In Arabidopsis thaliana the evolutionary and functional relationship between Leu biosynthesis and the Met chain elongation pathway, the first part of glucosinolate formation, is well documented. Nevertheless the exact functions of some pathway components are still unclear. Isopropylmalate isomerase (IPMI), an enzyme usually involved in Leu biosynthesis, is a heterodimer consisting of a large and a small subunit. While the large protein is encoded by a single gene (ISOPROPYLMALATE ISOMERASE LARGE SUBUNIT1), three genes encode small subunits (ISOPROPYLMALATE ISOMERASE SMALL SUBUNIT1 to 3). We have now analyzed small subunit 1 (ISOPROPYLMALATE ISOMERASE SMALL SUBUNIT1) employing artificial microRNA for a targeted knockdown of the encoding gene. Strong reduction of corresponding mRNA levels to less than 5% of wild-type levels resulted in a severe phenotype with stunted growth, narrow pale leaf blades with green vasculature and abnormal adaxial-abaxial patterning as well as anomalous flower morphology. Supplementation of the knockdown plants with leucine could only partially compensate for the morphological and developmental abnormalities. Detailed metabolite profiling of the knockdown plants revealed changes in the steady state levels of isopropylmalate and glucosinolates as well as their intermediates demonstrating a function of IPMI SSU1 in both leucine biosynthesis and the first cycle of Met chain elongation. Surprisingly the levels of free leucine slightly increased suggesting an imbalanced distribution of leucine within cells and/or within plant tissues.

The long-term effect of zinc soil contamination on selected free amino acids playing an important role in plant adaptation to stress and senescence

Increased endogenous plant cytokinin (CK) content through transformation with an isopentyl transferase (ipt) gene has been associated with improved plant stress tolerance. The objective of this study is to determine amino acid changes associated with elevated CK production in ipt transgenic tobacco (Nicotiana tabacum L., cv. Wisconsin 38). Nontransformed (WT) and transformed tobacco plants with ipt gene controlled by senescence-activated promoter (SAG) were exposed to zinc soil contamination (tested levels Zn1=250, Zn2=500, Zn3=750 mg kg(-1) soil). The Zn effect on plant stress metabolism resulted in changes in levels of selected free amino acids playing an important role in adaptation to stress and plant senescence (alanine, leucine, proline, methionine and γ-aminobutyrate) and differed for transformed and nontransformed tobacco plants. Analyses of amino acids confirmed that SAG tobacco plants had improved zinc tolerance compared with the WT plants. The enhanced Zn tolerance of SAG plants was associated with the maintenance of accumulation of proline, methionine and γ-aminobutyrate. The concentrations of leucine and alanine did not show significant differences between plant lines.

OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

BACKGROUND

Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.

RESULTS

The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.

CONCLUSION

The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.