Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging

Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures

Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

The Resistance of Oilseed Rape Microspore-Derived Embryos to Osmotic Stress Is Associated With the Accumulation of Energy Metabolism Proteins, Redox Homeostasis, Higher Abscisic Acid, and Cytokinin Contents

The present study aims to investigate the response of rapeseed microspore-derived embryos (MDE) to osmotic stress at the proteome level. The PEG-induced osmotic stress was studied in the cotyledonary stage of MDE of two genotypes: Cadeli (D) and Viking (V), previously reported to exhibit contrasting leaf proteome responses under drought. Two-dimensional difference gel electrophoresis (2D-DIGE) revealed 156 representative protein spots that have been selected for MALDI-TOF/TOF analysis. Sixty-three proteins have been successfully identified and divided into eight functional groups. Data are available via ProteomeXchange with identifier PXD024552. Eight selected protein accumulation trends were compared with real-time quantitative PCR (RT-qPCR). Biomass accumulation in treated D was significantly higher (3-fold) than in V, which indicates D is resistant to osmotic stress. Cultivar D displayed resistance strategy by the accumulation of proteins in energy metabolism, redox homeostasis, protein destination, and signaling functional groups, high ABA, and active cytokinins (CKs) contents. In contrast, the V protein profile displayed high requirements of energy and nutrients with a significant number of stress-related proteins and cell structure changes accompanied by quick downregulation of active CKs, as well as salicylic and jasmonic acids. Genes that were suitable for gene-targeting showed significantly higher expression in treated samples and were identified as phospholipase D alpha, peroxiredoxin antioxidant, and lactoylglutathione lyase. The MDE proteome profile has been compared with the leaf proteome evaluated in our previous study. Different mechanisms to cope with osmotic stress were revealed between the genotypes studied. This proteomic study is the first step to validate MDE as a suitable model for follow-up research on the characterization of new crossings and can be used for preselection of resistant genotypes.

Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L

Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.

Plastidial and cytosolic thiol reductases participate in the control of stomatal functioning

Stomatal movements via the control of gas exchanges determine plant growth in relation to environmental stimuli through a complex signalling network involving reactive oxygen species that lead to post-translational modifications of Cys and Met residues, and alter protein activity and/or conformation. Thiol-reductases (TRs), which include thioredoxins, glutaredoxins (GRXs) and peroxiredoxins (PRXs), participate in signalling pathways through the control of Cys redox status in client proteins. Their involvement in stomatal functioning remains poorly characterized. By performing a mass spectrometry-based proteomic analysis, we show that numerous thiol reductases, like PRXs, are highly abundant in guard cells. When investigating various Arabidopsis mutants impaired in the expression of TR genes, no change in stomatal density and index was noticed. In optimal growth conditions, a line deficient in cytosolic NADPH-thioredoxin reductases displayed higher stomatal conductance and lower leaf temperature evaluated by thermal infrared imaging. In contrast, lines deficient in plastidial 2-CysPRXs or type-II GRXs exhibited compared to WT reduced conductance and warmer leaves in optimal conditions, and enhanced stomatal closure in epidermal peels treated with abscisic acid or hydrogen peroxide. Altogether, these data strongly support the contribution of thiol redox switches within the signalling network regulating guard cell movements and stomatal functioning.

Guard cell redox proteomics reveals a role of lipid transfer protein in plant defense

Redox-based post-translational modifications (PTMs) involving protein cysteine residues as redox sensors are important to various physiological processes. However, little is known about redox-sensitive proteins in guard cells and their functions in stomatal immunity. In this study, we applied an integrative protein labeling method cysTMTRAQ, and identified guard cell proteins that were altered by thiol redox PTMs in response to a bacterial flagellin peptide flg22. In total, eight, seven and 20 potential redox-responsive proteins were identified in guard cells treated with flg22 for 15, 30 and 60 min, respectively. The proteins fall into several functional groups including photosynthesis, lipid binding, oxidation-reduction, and defense. Among the proteins, a lipid transfer protein (LTP)-II was confirmed to be redox-responsive and involved in plant resistance to Pseudomonas syringe pv. tomato DC3000. This study not only creates an inventory of potential redox-sensitive proteins in flg22 signal transduction in guard cells, but also highlights the biological relevance of the lipid transfer protein in plant defense against bacterial pathogens. SIGNIFICANCE: Protein redox modifications play important roles in many physiological processes. However, redox proteomics has rarely been studied in plant single cell-types. In this study, isobaric tandem mass tag-based redox proteomics technology was applied to discover redox-sensitive proteins and corresponding cysteine residues in guard cell response to a bacterial flagellin peptide flg22. Many redox-responsive proteins related to photosynthesis, lipid binding, oxidation-reduction, and defense were identified. Using reverse genetics and biochemical analyses, a lipid transfer protein was functionally characterized to be involved in plant defense against pathogens. The study highlights the utility of redox proteomics in discovering new proteins and redox modifications in important stomatal guard cell functions. Furthermore, detailed functional characterization demonstrates the biological relevance of the redox-responsive lipid transfer protein in plant pathogen defense.

Roles of the Brassica napus DELLA Protein BnaA6.RGA, in Modulating Drought Tolerance by Interacting With the ABA Signaling Component BnaA10.ABF2

Drought is a major threat to plant growth and crop productivity. Reduced level of the gibberellin would result in increased drought tolerance, but the underlying mechanism is still unclear. In Brassica napus, there are four BnaRGA genes that code for DELLA proteins, negative regulators of GA signaling. Among them, expression of BnaA6.RGA was greatly induced by drought and abscisic acid (ABA). Previously, we created the gain-of-function mutant of BnaA6.RGA, bnaa6.rga-D, and the loss-of-function quadruple mutant, bnarga by CRISPR/Cas9, respectively. Here we show that bnaa6.rga-D displayed enhanced drought tolerance, and its stomatal closure was hypersensitive to ABA treatment. By contrast, bnarga displayed reduced drought tolerance and was less sensitive to ABA treatment, but there is no difference in drought tolerance between single BnaRGA mutant and WT, suggesting a functional redundancy between the BnaRGA genes in this process. Furthermore, we found that BnaRGAs were able to interact physically with BnaA10.ABF2, an essential transcription factor in ABA signaling. The BnaA10.ABF2-BnaA6.RGA protein complex greatly increased the expression level of the drought responsive gene BnaC9.RAB18. Taken together, this work highlighted the fundamental roles of DELLA proteins in drought tolerance in B. napus, and provide desirable germplasm for further breeding of drought tolerance in rapeseed.

iTRAQ-Based Quantitative Analysis of Responsive Proteins Under PEG-Induced Drought Stress in Wheat Leaves

Drought is an important abiotic stress that seriously restricts crop productivity. An understanding of drought tolerance mechanisms offers guidance for cultivar improvement. In order to understand how a well-known wheat genotype Jinmai 47 responds to drought, we adopted the iTRAQ and LC/MS approaches and conducted proteomics analysis of leaves after exposure to 20% of polyethylene glycol-6000 (PEG)-induced stress for 4 days. The study identified 176 differentially expressed proteins (DEPs), with 65 (36.5%) of them being up-regulated, and 111 (63.5%) down-regulated. DEPs, located in cellular membranes and cytosol mainly, were involved in stress and redox regulation (51), carbohydrate and energy metabolism (36), amino acid metabolism (24), and biosynthesis of other secondary metabolites (20) primarily. Under drought stress, TCA cycle related proteins were up-regulated. Antioxidant system, signaling system, and nucleic acid metabolism etc. were relatively weakened. In comparison, the metabolism pathways that function in plasma dehydration protection and protein structure protection were strongly enhanced, as indicated by the improved biosynthesis of 2 osmolytes, sucrose and Proline, and strongly up-regulated protective proteins, LEA proteins and chaperones. SUS4, P5CSs, OAT, Rab protein, and Lea14-A were considered to be important candidate proteins, which deserve to be further investigated.

iTRAQ-Based Identification of Proteins Related to Lignin Synthesis in the Pear Pollinated with Pollen from Different Varieties

Most pears in Anhui Province are a kind of self-incompatible fruit whose quality is strongly influenced by the male pollen. The proteomic variation of Dangshan Su pollinated by different varieties was analysed using the isobaric tag for relative and absolute quantitation (iTRAQ) to investigate the effect of pollination by different varieties on the pear lignin pathway. Among the 3980 proteins identified from the two samples, 139 proteins were identified as differentially expressed proteins (DEPs). Of these proteins, laccase-4 (LAC4), was found to be related with lignin synthesis, and β-glucosidase 15 (BGLU15) and peroxidase 47 (PER47) were involved in the phenylpropanoid pathway. Moreover, the lignin and stone cell contents were lower in DW (Dangshan Su pollinated by Wonhwang) than those in DJ (Dangshan Su pollinated by Jingbaili). The effect of pollination on the synthesis of lignin through the regulation of the expression of PER47, BGLU15 and LAC4 ultimately affects the formation of stone cells and the fruit quality. We report for the first time that different pollinations influence the protein expression profile in the Dangshan Su pear, and this result provides some new epididymal targets for regulating the synthesis of lignin, regulating the content of stone cells and improving the quality of the pears.

Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses

Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of ¹³ C/¹⁵ N-lysine and ¹³ C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.

Plant Systems Biology at the Single-Cell Level

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.

Metabolic Signatures in Response to Abscisic Acid (ABA) Treatment in Brassica napus Guard Cells Revealed by Metabolomics

Drought can severely damage crops, resulting in major yield losses. During drought, vascular land plants conserve water via stomatal closure. Each stomate is bordered by a pair of guard cells that shrink in response to drought and the associated hormone abscisic acid (ABA). The activation of complex intracellular signaling networks underlies these responses. Therefore, analysis of guard cell metabolites is fundamental for elucidation of guard cell signaling pathways. Brassica napus is an important oilseed crop for human consumption and biodiesel production. Here, non-targeted metabolomics utilizing gas chromatography mass spectrometry (GC-MS/MS) and liquid chromatography mass spectrometry (LC-MS/MS) were employed for the first time to identify metabolic signatures in response to ABA in B. napus guard cell protoplasts. Metabolome profiling identified 390 distinct metabolites in B. napus guard cells, falling into diverse classes. Of these, 77 metabolites, comprising both primary and secondary metabolites were found to be significantly ABA responsive, including carbohydrates, fatty acids, glucosinolates, and flavonoids. Selected secondary metabolites, sinigrin, quercetin, campesterol, and sitosterol, were confirmed to regulate stomatal closure in Arabidopsis thaliana, B. napus or both species. Information derived from metabolite datasets can provide a blueprint for improvement of water use efficiency and drought tolerance in crops.

Metabolomics and Proteomics of Brassica napus Guard Cells in Response to Low CO2

Stomatal guard cell response to various stimuli is an important process that balances plant carbon dioxide (CO2) uptake and water transpiration. Elevated CO2 induces stomatal closure, while low CO2 promotes stomatal opening. The signaling process of elevated CO2 induced stomatal closure has been extensively studied in recent years. However, the mechanism of low CO2 induced stomatal opening is not fully understood. Here we report metabolomic and proteomic responses of Brassica napus guard cells to low CO2 using hyphenated mass spectrometry technologies. A total of 411 metabolites and 1397 proteins were quantified in a time-course study of low CO2 effects. Metabolites and proteins that exhibited significant changes are overrepresented in fatty acid metabolism, starch and sucrose metabolism, glycolysis and redox regulation. Concomitantly, multiple hormones that promote stomatal opening increased in response to low CO2. Interestingly, jasmonic acid precursors were diverted to a branch pathway of traumatic acid biosynthesis. These results indicate that the low CO2 response is mediated by a complex crosstalk between different phytohormones.

Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses

BACKGROUND

Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry (Cerasus humilis) is a good perennial plant for studying the physiological and sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants.

METHODS

Currently, physiological parameters were applied to investigate C. humilis response to WD. Moreover, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in C. humilis leaves subjected to WD (24 d). Furthermore, we also examined the correlation between protein and transcript levels.

RESULTS

Several physiological parameters, including relative water content and Pn were reduced by WD. In addition, the malondialdehyde (MDA), relative electrolyte leakage (REL), total soluble sugar, and proline were increased in WD-treated C. humilis. Comparative proteomic analysis revealed 46 protein spots (representing 43 unique proteins) differentially expressed in C. humilis leaves under WD. These proteins were mainly involved in photosynthesis, ROS scavenging, carbohydrate metabolism, transcription, protein synthesis, protein processing, and nitrogen and amino acid metabolisms, respectively.

CONCLUSIONS

WD promoted the CO2 assimilation by increase light reaction and Calvin cycle, leading to the reprogramming of carbon metabolism. Moreover, the accumulation of osmolytes (i.e., proline and total soluble sugar) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione s-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under WD. Importantly, the regulation role of carbohydrate metabolisms (e. g. glycolysis, pentose phosphate pathways, and TCA) was enhanced. These findings provide key candidate proteins for genetic improvement of perennial plants metabolism under WD.

Effect of foliar application of plant growth regulators on nitrous oxide (N2O) emission and grain yield in wheat

Agricultural soils are the major source of global nitrous oxide (N₂O) emission, and more than two thirds of N₂O emission originate from soil. Recent studies have identified that green plants contribute to transport of N₂O to the atmosphere. We investigated the effects of foliar application of plant growth regulators (PGRs) and growth stimulating chemicals on N₂O emission and wheat grain yield for 2 years. The PGRs' abscisic acid (ABA) and cytozyme (20 mg L^-1), kinetin (10 and 20 mg L^-1) and wet tea extract (1:20 w/w) along with distilled water as control were sprayed on wheat canopy at the tillering and panicle initiation stages. Our results showed that cytozyme and tea extract enhanced the plant dry biomass over control. Kinetin (10 and 20 mg L^-1) and cytozyme increased the plant photosynthetic rate and photosynthate partitioning towards the developing grain. ABA (20 mg L^-1) and kinetin (10 and 20 mg L^-1) reduced the N₂O emission over control primarily through regulation of leaf growth, stomatal density and xylem vessel size. Leaf area, stomatal density and xylem vessel size were found to be associated with N₂O transport and emission. We concluded that use of ABA and kinetin can reduce N₂O emissions without any impact on wheat grain yield.

Bicarbonate Induced Redox Proteome Changes in Arabidopsis Suspension Cells

Climate change as a result of increasing atmospheric CO₂ affects plant growth and productivity. CO₂ is not only a carbon donor for photosynthesis but also an environmental signal that can perturb cellular redox homeostasis and lead to modifications of redox-sensitive proteins. Although redox regulation of protein functions has emerged as an important mechanism in several biological processes, protein redox modifications and how they function in plant CO₂ response remain unclear. Here a new iodoTMTRAQ proteomics technology was employed to analyze changes in protein redox modifications in Arabidopsis thaliana suspension cells in response to bicarbonate (mimic of elevated CO₂) in a time-course study. A total of 47 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism, transport, ROS scavenging, cell structure modulation and protein turnover. This inventory of previously unknown redox responsive proteins in Arabidopsis bicarbonate responses lays a foundation for future research toward understanding the molecular mechanisms underlying plant CO₂ responses.

Jasmonate-mediated stomatal closure under elevated CO2 revealed by time-resolved metabolomics

Foliar stomatal movements are critical for regulating plant water loss and gas exchange. Elevated carbon dioxide (CO₂ ) levels are known to induce stomatal closure. However, the current knowledge on CO₂ signal transduction in stomatal guard cells is limited. Here we report metabolomic responses of Brassica napus guard cells to elevated CO₂ using three hyphenated metabolomics platforms: gas chromatography-mass spectrometry (MS); liquid chromatography (LC)-multiple reaction monitoring-MS; and ultra-high-performance LC-quadrupole time-of-flight-MS. A total of 358 metabolites from guard cells were quantified in a time-course response to elevated CO₂ level. Most metabolites increased under elevated CO₂ , showing the most significant differences at 10 min. In addition, reactive oxygen species production increased and stomatal aperture decreased with time. Major alterations in flavonoid, organic acid, sugar, fatty acid, phenylpropanoid and amino acid metabolic pathways indicated changes in both primary and specialized metabolic pathways in guard cells. Most interestingly, the jasmonic acid (JA) biosynthesis pathway was significantly altered in the course of elevated CO₂ treatment. Together with results obtained from JA biosynthesis and signaling mutants as well as CO₂ signaling mutants, we discovered that CO₂ -induced stomatal closure is mediated by JA signaling.

Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy

The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level.

SIGNIFICANCE

Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.

Molecular and systems approaches towards drought-tolerant canola crops

1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.

Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα)

Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription.

Genome-wide identification and homeolog-specific expression analysis of the SnRK2 genes in Brassica napus guard cells

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) proteins constitute a small plant-specific serine/threonine kinase family involved in abscisic acid (ABA) signaling and plant responses to biotic and abiotic stresses. Although SnRK2s have been well-studied in Arabidopsis thaliana, little is known about SnRK2s in Brassica napus. Here we identified 30 putative sequences encoding 10 SnRK2 proteins in the B. napus genome and the expression profiles of a subset of 14 SnRK2 genes in guard cells of B. napus. In agreement with its polyploid origin, B. napus maintains both homeologs from its diploid parents. The results of quantitative real-time PCR (qRT-PCR) and reanalysis of RNA-Seq data showed that certain BnSnRK2 genes were commonly expressed in leaf tissues in different varieties of B. napus. In particular, qRT-PCR results showed that 12 of the 14 BnSnRK2s responded to drought stress in leaves and in ABA-treated guard cells. Among them, BnSnRK2.4 and BnSnRK2.6 were of interest because of their robust responsiveness to ABA treatment and drought stress. Notably, BnSnRK2 genes exhibited up-regulation of different homeologs, particularly in response to abiotic stress. The homeolog expression bias in BnSnRK2 genes suggests that parental origin of genes might be responsible for efficient regulation of stress responses in polyploids. This work has laid a foundation for future functional characterization of the different BnSnKR2 homeologs in B. napus and its parents, especially their functions in guard cell signaling and stress responses.

Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.

New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants

Glucosinolates present in Brassicales are important for human health and plant defense against insects and pathogens. Here we investigate the proteomes and metabolomes of Arabidopsis myb28/29 and cyp79B2/B3 mutants deficient in aliphatic glucosinolates and indolic glucosinolates, respectively. Quantitative proteomics of the myb28/29 and cyp79B2/B3 mutants led to the identification of 2785 proteins, of which 142 proteins showed significant changes in the two mutants compared to wild type (WT). By mapping the differential proteins using STRING, we detected 59 new edges in the glucosinolate metabolic network. These connections can be classified as primary with direct roles in glucosinolate metabolism, secondary related to plant stress responses, and tertiary involved in other biological processes. Gene Ontology analysis of the differential proteins showed high level of enrichment in the nodes belonging to metabolic process including glucosinolate biosynthesis and response to stimulus. Using metabolomics, we quantified 292 metabolites covering a broad spectrum of metabolic pathways, and 89 exhibited differential accumulation patterns between the mutants and WT. The changing metabolites (e.g., γ-glutamyl amino acids, auxins and glucosinolate hydrolysis products) complement our proteomics findings. This study contributes toward engineering and breeding of glucosinolate profiles in plants in efforts to improve human health, crop quality and productivity.

BIOLOGICAL SIGNIFICANCE

Glucosinolates in Brassicales constitute an important group of natural metabolites important for plant defense and human health. Its biosynthetic pathways and transcriptional regulation have been well-studied. Using Arabidopsis mutants of important genes in glucosinolate biosynthesis, quantitative proteomics and metabolomics led to identification of many proteins and metabolites that are potentially related to glucosinolate metabolism. This study provides a comprehensive insight into the molecular networks of glucosinolate metabolism, and will facilitate efforts toward engineering and breeding of glucosinolate profiles for enhanced crop defense, and nutritional value.

Protein Phosphorylation and Redox Modification in Stomatal Guard Cells

Post-translational modification (PTM) is recognized as a major process accounting for protein structural variation, functional diversity, and the dynamics and complexity of the proteome. Since PTMs can change the structure and function of proteins, they are essential to coordinate signaling networks and to regulate important physiological processes in eukaryotes. Plants are constantly challenged by both biotic and abiotic stresses that reduce productivity, causing economic losses in crops. The plant responses involve complex physiological, cellular, and molecular processes, with stomatal movement as one of the earliest responses. In order to activate such a rapid response, stomatal guard cells employ cellular PTMs of key protein players in the signaling pathways to regulate the opening and closure of the stomatal pores. Here we discuss two major types of PTMs, protein phosphorylation and redox modification that play essential roles in stomatal movement under stress conditions. We present an overview of PTMs that occur in stomatal guard cells, especially the methods and technologies, and their applications in PTM identification and quantification. Our focus is on PTMs that modify molecular components in guard cell signaling at the stages of signal perception, second messenger production, as well as downstream signaling events and output. Improved understanding of guard cell signaling will enable generation of crops with enhanced stress tolerance, and increased yield and bioenergy through biotechnology and molecular breeding.

Preparation of Epidermal Peels and Guard Cell Protoplasts for Cellular, Electrophysiological, and -Omics Assays of Guard Cell Function

Bioassays are commonly used to study stomatal phenotypes. There are multiple options in the choice of plant materials and species used for observation of stomatal and guard cell responses in vivo. Here, detailed procedures for bioassays of stomatal responses to abscisic acid (ABA) in Arabidopsis thaliana are described, including ABA promotion of stomatal closure, ABA inhibition of stomatal opening, and ABA promotion of reaction oxygen species (ROS) production in guard cells. We also include an example of a stomatal bioassay for the guard cell CO2 response using guard cell-enriched epidermal peels from Brassica napus. Highly pure preparations of guard cell protoplasts can be produced, which are also suitable for studies on guard cell signaling, as well as for studies on guard cell ion transport. Small-scale and large-scale guard cell protoplast preparations are commonly used for electrophysiological and -omics studies, respectively. We provide a procedure for small-scale guard cell protoplasting from A. thaliana. Additionally, a general protocol for large-scale preparation of guard cell protoplasts, with specifications for three different species, A. thaliana, B. napus, and Vicia faba is also provided.

Role of the proteome in phytohormonal signaling

Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Identification of thioredoxin targets in guard cell enriched epidermal peels using cysTMT proteomics

Thioredoxins (Trx) play central roles in cellular redox regulation. Although hundreds of Trx targets have been identified using different approaches, the capture of targets in a quantitative and efficient manner is challenging. Here we report a high-throughput method using cysteine reactive tandem mass tag (cysTMT) labeling followed by liquid chromatography (LC)-mass spectrometry (MS) to screen for Trx targets. Compared to existing methods, this approach allows for i) three replicates of pairwise comparison in a single LC-MS run to reduce run-to-run variation; ii) efficient enrichment of cysteine-containing peptides that requires low protein input; and iii) accurate quantification of the cysteine redox status and localization of the Trx targeted cysteine residues. Application of this method in guard cell-enriched epidermal peels from Brassica napus revealed 80 Trx h targets involved in a broad range of processes, including photosynthesis, stress response, metabolism and cell signaling. The adaption of this protocol in other systems will greatly improve our understanding of the Trx function in regulating cellular redox homeostasis.

BIOLOGICAL SIGNIFICANCE

Redox homeostasis is tightly regulated for proper cellular activities. Specific protein-protein interactions between redox active molecules such as thioredoxin (Trx) and target proteins constitute the basis for redox-regulated biological processes. The use of cysTMT quantitative proteomics for studying Trx reactions enabled identification of potential Trx targets that provide important insights into the redox regulation in guard cells, a specialized plant cell type responsible for sensing of environmental signals, gas exchange and plant productivity.

Tobacco guard cells fix CO2 by both Rubisco and PEPcase while sucrose acts as a substrate during light-induced stomatal opening

Transcriptomic and proteomic studies have improved our knowledge of guard cell function; however, metabolic changes in guard cells remain relatively poorly understood. Here we analysed metabolic changes in guard cell-enriched epidermal fragments from tobacco during light-induced stomatal opening. Increases in sucrose, glucose and fructose were observed during light-induced stomatal opening in the presence of sucrose in the medium while no changes in starch were observed, suggesting that the elevated fructose and glucose levels were a consequence of sucrose rather than starch breakdown. Conversely, reduction in sucrose was observed during light- plus potassium-induced stomatal opening. Concomitant with the decrease in sucrose, we observed an increase in the level as well as in the (13) C enrichment in metabolites of, or associated with, the tricarboxylic acid cycle following incubation of the guard cell-enriched preparations in (13) C-labelled bicarbonate. Collectively, the results obtained support the hypothesis that sucrose is catabolized within guard cells in order to provide carbon skeletons for organic acid production. Furthermore, they provide a qualitative demonstration that CO2 fixation occurs both via ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPcase). The combined data are discussed with respect to current models of guard cell metabolism and function.

Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control

Stomata control the concomitant exchange of CO2 and transpiration in land plants. While a constant supply of CO2 is need to maintain the rate of photosynthesis, the accompanying water losses must be tightly regulated to prevent dehydration and undesired metabolic changes. The factors affecting stomatal movement are directly coupled with the cellular networks of guard cells. Although the guard cell has been used as a model for characterization of signaling pathways, several important questions about its functioning remain elusive. Current modeling approaches describe the stomatal conductance in terms of relatively few easy-to-measure variables being unsuitable for in silico design of genetic manipulation strategies. Here, we argue that a system biology approach, combining modeling and high-throughput experiments, may be used to elucidate the mechanisms underlying stomata control and to determine targets for modulation of stomatal responses to environment. In support of our opinion, we review studies demonstrating how high-throughput approaches have provided a systems-view of guard cells. Finally, we emphasize the opportunities and challenges of genome-scale modeling and large-scale data integration for in silico manipulation of guard cell functions to improve crop yields, particularly under stress conditions which are of pertinence both to climate change and water use efficiency.

Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress

Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions.

Proteome analysis of pear reveals key genes associated with fruit development and quality

Comparative and association analyses of the proteome and transcriptome for pear fruit development were conducted for the first time in this study. Pear fruit development involves complex physiological and biochemical processes, but there is still little knowledge available at proteomic and transcriptomic levels, which would be helpful for understanding the molecular mechanisms of fruit development and quality in pear. In our study, three important stages, including early development (S4-22), middle development (S6-27), and near ripening (S8-30), were investigated in 'Dangshansuli' by isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology, identifying a total of 1,810 proteins during pear fruit development. The association analysis of proteins and transcript expression revealed 1,724, 1,722, and 1,718 associated proteins identified in stages S4-22, S6-27, and S8-30, respectively. A total of 237, 318, and 425 unique proteins were identified as differentially expressed during S4-22 vs S6-27, S6-27 vs S8-30, S4-22 vs S8-30, respectively, and the corresponding correlation coefficients of the overall differentially expressed proteins and transcripts data were 0.6336, 0.4113, and 0.7049. The phenylpropanoid biosynthesis pathway, which is related to lignin formation of pear fruit, was identified as a significantly enriched pathway during early stages of fruit development. Finally, a total of 35 important differentially expressed proteins related to fruit quality were identified, including three proteins related to sugar formation, seven proteins related to aroma synthesis, and sixteen proteins related to the formation of lignin. In addition, qRT-PCR verification provided further evidence to support differentially expressed gene selection. This study is the first to reveal protein and associated mRNA variations in pear during fruit development and quality conformation, and identify key genes and proteins helpful for future functional genomics studies, and provides gene resources for improvement of pear quality.

The guard cell metabolome: functions in stomatal movement and global food security

Guard cells represent a unique single cell-type system for the study of cellular responses to abiotic and biotic perturbations that affect stomatal movement. Decades of effort through both classical physiological and functional genomics approaches have generated an enormous amount of information on the roles of individual metabolites in stomatal guard cell function and physiology. Recent application of metabolomics methods has produced a substantial amount of new information on metabolome control of stomatal movement. In conjunction with other "omics" approaches, the knowledge-base is growing to reach a systems-level description of this single cell-type. Here we summarize current knowledge of the guard cell metabolome and highlight critical metabolites that bear significant impact on future engineering and breeding efforts to generate plants/crops that are resistant to environmental challenges and produce high yield and quality products for food and energy security.

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.

A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize

In maize developing seeds, transfer cells are prominently located at the basal endosperm transfer layer (BETL). As the first filial cell layer, BETL is a gateway to sugars, nutrients and water from mother plant; and anchor of numerous functions such as sucrose turnover, auxin and cytokinin biosynthesis/accumulation, energy metabolism, defense response, and signaling between maternal and filial generations. Previous studies showed that basal developing endosperms of miniature1 (mn1) mutant seeds lacking the Mn1-encoded cell wall invertase II, are also deficient for hexose. Given the role of glucose as one of the key sugars in protein glycosylation and proper protein folding; we performed a comparative large scale glycoproteome profiling of total proteins of these two genotypes (mn1 mutant vs. Mn1 wild type) using 2D gel electrophoresis and glycosylation/total protein staining, followed by image analysis. Protein identification was done by LC-MS/MS. A total of 413 spots were detected; from which, 113 spots matched between the two genotypes. Of these, 45 showed >20% decrease/increase in glycosylation level and were selected for protein identification. A large number of identified proteins showed decreased glycosylation levels in mn1 developing endosperms as compared to the Mn1. Functional classification of proteins, showed mainly of post-translational modification, protein turnover, chaperone activities, carbohydrate and amino acid biosynthesis/transport, and cell wall biosynthesis. These proteins and activities were related to endoplasmic reticulum (ER) stress and unfolded protein response (UPR) as a result of the low glycolsylation levels of the mutant proteins. Overall, these results provide for the first time a global glycoproteome profile of maize BETL-enriched basal endosperm to better understand their role in seed development in maize.

Comprehensive cell-specific protein analysis in early and late pollen development from diploid microsporocytes to pollen tube growth

Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development.

iTRAQ-based quantitative proteomics of developing and ripening muscadine grape berry

Grapes are among the widely cultivated fruit crops in the world. Grape berries like other nonclimacteric fruits undergo a complex set of dynamic, physical, physiological, and biochemical changes during ripening. Muscadine grapes are widely cultivated in the southern United States for fresh fruit and wine. To date, changes in the metabolites composition of muscadine grapes have been well documented; however, the molecular changes during berry development and ripening are not fully known. The aim of this study was to investigate changes in the berry proteome during ripening in muscadine grape cv. Noble. Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS was used to detect statistically significant changes in the berry proteome. A total of 674 proteins were detected, and 76 were differentially expressed across four time points in muscadine berry. Proteins obtained were further analyzed to provide information about its potential functions during ripening. Several proteins involved in abiotic and biotic stimuli and sucrose and hexose metabolism were upregulated during berry ripening. Quantitative real-time PCR analysis validated the protein expression results for nine proteins. Identification of vicilin-like antimicrobial peptides indicates additional disease tolerance proteins are present in muscadines for berry protection during ripening. The results provide new information for characterization and understanding muscadine berry proteome and grape ripening.

Abscisic acid-responsive guard cell metabolomes of Arabidopsis wild-type and gpa1 G-protein mutants

Individual metabolites have been implicated in abscisic acid (ABA) signaling in guard cells, but a metabolite profile of this specialized cell type is lacking. We used liquid chromatography-multiple reaction monitoring mass spectrometry for targeted analysis of 85 signaling-related metabolites in Arabidopsis thaliana guard cell protoplasts over a time course of ABA treatment. The analysis utilized ∼ 350 million guard cell protoplasts from ∼ 30,000 plants of the Arabidopsis Columbia accession (Col) wild type and the heterotrimeric G-protein α subunit mutant, gpa1, which has ABA-hyposensitive stomata. These metabolomes revealed coordinated regulation of signaling metabolites in unrelated biochemical pathways. Metabolites clustered into different temporal modules in Col versus gpa1, with fewer metabolites showing ABA-altered profiles in gpa1. Ca(2+)-mobilizing agents sphingosine-1-phosphate and cyclic adenosine diphosphate ribose exhibited weaker ABA-stimulated increases in gpa1. Hormone metabolites were responsive to ABA, with generally greater responsiveness in Col than in gpa1. Most hormones also showed different ABA responses in guard cell versus mesophyll cell metabolomes. These findings suggest that ABA functions upstream to regulate other hormones, and are also consistent with G proteins modulating multiple hormonal signaling pathways. In particular, indole-3-acetic acid levels declined after ABA treatment in Col but not gpa1 guard cells. Consistent with this observation, the auxin antagonist α-(phenyl ethyl-2-one)-indole-3-acetic acid enhanced ABA-regulated stomatal movement and restored partial ABA sensitivity to gpa1.

Proteomic comparison of basal endosperm in maize miniature1 mutant and its wild-type Mn1

Developing endosperm in maize seed is a major site for biosynthesis and storage of starch and proteins, and of immense economic importance for its role in food, feed and biofuel production. The basal part of endosperm performs a major role in solute, water and nutrition acquisition from mother plant to sustain these functions. The miniature1 (mn1) mutation is a loss-of-function mutation of the Mn1-encoded cell wall invertase that is entirely expressed in the basal endosperm and is essential for many of the metabolic and signaling functions associated with metabolically released hexose sugars in developing endosperm. Here we report a comparative proteomic study between Mn1 and mn1 basal endosperm to better understand basis of pleiotropic effects on many diverse traits in the mutant. Specifically, we used iTRAQ based quantitative proteomics combined with Gene Ontology (GO) and bioinformatics to understand functional basis of the proteomic information. A total of 2518 proteins were identified from soluble and cell wall associated protein (CWAP) fractions; of these 131 proteins were observed to be differentially expressed in the two genotypes. The main functional groups of proteins that were significantly different were those involved in the carbohydrate metabolic and catabolic process, and cell homeostasis. The study constitutes the first proteomic analysis of basal endosperm cell layers in relation to endosperm growth and development in maize.

Single-cell-type proteomics: toward a holistic understanding of plant function

Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the protein characteristics of each type of cell will not only reveal specific cell functions, but also enhance understanding of how an organism works. Most plant proteomics studies have focused on using tissues and organs containing a mixture of different cells. Recent single-cell-type proteomics efforts on pollen grains, guard cells, mesophyll cells, root hairs, and trichomes have shown utility. We expect that high resolution proteomic analyses will reveal novel functions in single cells. This review provides an overview of recent developments in plant single-cell-type proteomics. We discuss application of the approach for understanding important cell functions, and we consider the technical challenges of extending the approach to all plant cell types. Finally, we consider the integration of single-cell-type proteomics with transcriptomics and metabolomics with the goal of providing a holistic understanding of plant function.

Proteomics and metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis

To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Proteins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the proteomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate metabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.

Methyl jasmonate responsive proteins in Brassica napus guard cells revealed by iTRAQ-based quantitative proteomics

Stomata on leaf epidermis formed by pairs of guard cells control CO(2) intake and water transpiration, and respond to different environmental conditions. Stress-induced stomatal closure is mediated via an intricate hormone network in guard cells. Although methyl jasmonate (MeJA) has been intensively studied for its function in plant defense, the molecular mechanisms underlying its function in stomatal movement are not fully understood. Here we report the effects of MeJA on Brassica napus stomatal movement and H(2)O(2) production. Using the isobaric tags for relative and absolute quantitation (iTRAQ) approach, we have identified 84 MeJA-responsive proteins in B. napus guard cells. Most of the genes encoding these proteins contain jasmonate-responsive elements in the promoters, indicating that they are potentially regulated at the transcriptional level. Among the identified proteins, five protein changes after MeJA treatment were validated using Western blot analysis. The identification of the MeJA-responsive proteins has revealed interesting molecular mechanisms underlying MeJA function in guard cells, which include homeostasis of H(2)O(2) production and scavenging, signaling through calcium oscillation and protein (de)phosphorylation, gene transcription, protein modification, energy balance, osmoregulation, and cell shape modulation. The knowledge of the MeJA-responsive proteins has improved our understanding of MeJA signaling in stomatal movement, and it may be applied to crop engineering for enhanced yield and stress tolerance.

Glucocorticoids and histone deacetylase inhibitors cooperate to block the invasiveness of basal-like breast cancer cells through novel mechanisms

Aggressive cancers often express E-cadherin in cytoplasmic vesicles rather than on the plasma membrane and this may contribute to the invasive phenotype of these tumors. Therapeutic strategies are not currently available that restore the anti-invasive function of E-cadherin in cancers. MDA-MB-231 cells are a frequently used model of invasive triple-negative breast cancer, and these cells express low levels of E-cadherin that is mislocalized to cytoplasmic vesicles. MDA-MB-231 cell lines stably expressing wild-type E-cadherin or E-cadherin fused to glutathione S-transferase or green fluorescent protein were used as experimental systems to probe the mechanisms responsible for cytoplasmic E-cadherin localization in invasive cancers. Although E-cadherin expression partly reduced cell invasion in vitro, E-cadherin was largely localized to the cytoplasm and did not block the invasiveness of the corresponding orthotopic xenograft tumors. Further studies indicated that the glucocorticoid dexamethasone and the highly potent class I histone deacetylase (HDAC) inhibitor largazole cooperated to induce E-cadherin localization to the plasma membrane in triple-negative breast cancers, and to suppress cellular invasion in vitro. Dexamethasone blocked the production of the cleaved form of the CDCP1 (that is, CUB domain-containing protein 1) protein (cCDCP1) previously implicated in the pro-invasive activities of CDCP1 by upregulating the serine protease inhibitor plasminogen activator inhibitor-1. E-cadherin preferentially associated with cCDCP1 compared with the full-length form. In contrast, largazole did not influence CDCP1 cleavage, but increased the association of E-cadherin with γ-catenin. This effect on E-cadherin/γ-catenin complexes was shared with the nonisoform selective HDAC inhibitors trichostatin A (TSA) and vorinostat (suberoylanilide hydroxamic acid, SAHA), although largazole upregulated endogenous E-cadherin levels more strongly than TSA. These results demonstrate that glucocorticoids and HDAC inhibitors, both of which are currently in clinical use, cooperate to suppress the invasiveness of breast cancer cells through novel, complementary mechanisms that converge on E-cadherin.

Identification and characterization of interactions between abscisic acid and mitochondrial adenine nucleotide translocators

ABA (abscisic acid) is a plant hormone involved in important processes including development and stress responses. Recent reports have identified a number of plant ABA receptors and transporters, highlighting novel mechanisms of ABA action. In the present paper we describe application of a chemical proteomics approach leading to the identification of mitochondrial ANTs (adenine nucleotide translocators) as ABA-interacting proteins. Initial in vitro studies confirmed inhibition of ANT-dependent ATP translocation by ABA. Further analysis demonstrated ANT-dependent uptake of ABA into both recombinant Arabidopsis thaliana ANT2-containing proteoliposomes and native isolated spinach mitochondria; the latter with a Km of 3.5 μM and a Vmax of 2.5 nmol/min per g of protein. ATP was found to inhibit ANT-dependent ABA translocation. Specificity profiles highlight the possibility of mechanistic differences in translocation of ABA and ATP. Finally, ABA was shown to stimulate ATPase activity in spinach mitochondrial extracts. ABA concentrations in plant cells are estimated to reach the low micromolar range during stress responses, supporting potential physiological relevance of these in vitro findings. Overall, the present in vitro work suggests the possibility of as yet uncharacterized mechanisms of ABA action in planta related to inhibition of mitochondrial ATP translocation and functional localization of ABA in the mitochondrial matrix.