Quantitative plant proteomics

AAO2 impairment enhances aldehyde detoxification by AAO3 in Arabidopsis leaves exposed to UV-C or Rose-Bengal

Among the three active aldehyde oxidases in Arabidopsis thaliana leaves (AAO1-3), AAO3, which catalyzes the oxidation of abscisic-aldehyde to abscisic-acid, was shown recently to function as a reactive aldehyde detoxifier. Notably, aao2KO mutants exhibited less senescence symptoms and lower aldehyde accumulation, such as acrolein, benzaldehyde, and 4-hydroxyl-2-nonenal (HNE) than in wild-type leaves exposed to UV-C or Rose-Bengal. The effect of AAO2 expression absence on aldehyde detoxification by AAO3 and/or AAO1 was studied by comparing the response of wild-type plants to the response of single-functioning aao1 mutant (aao1S), aao2KO mutants, and single-functioning aao3 mutants (aao3Ss). Notably, aao3Ss exhibited similar aldehyde accumulation and chlorophyll content to aao2KO treated with UV-C or Rose-Bengal. In contrast, wild-type and aao1S exhibited higher aldehyde accumulation that resulted in lower remaining chlorophyll than in aao2KO leaves, indicating that the absence of active AAO2 enhanced AAO3 detoxification activity in aao2KO mutants. In support of this notion, employing abscisic-aldehyde as a specific substrate marker for AAO3 activity revealed enhanced AAO3 activity in aao2KO and aao3Ss leaves compared to wild-type treated with UV-C or Rose-Bengal. The similar abscisic-acid level accumulated in leaves of unstressed or stressed genotypes indicates that aldehyde detoxification by AAO3 is the cause for better stress resistance in aao2KO mutants. Employing the sulfuration process (known to activate aldehyde oxidases) in wild-type, aao2KO, and molybdenum-cofactor sulfurase (aba3-1) mutant plants revealed that the active AAO2 in WT employs sulfuration processes essential for AAO3 activity level, resulting in the lower AAO3 activity in WT than AAO3 activity in aao2KO.

Proteomics Approach to Differentiate Protein Extraction Methods in Sugar Beet Leaves

Interest in alternative plant-based protein sources is continuously growing. Sugar beet leaves have the potential to satisfy that demand due to their high protein content. They are considered as agricultural waste and utilizing them as protein sources can bring them back to the food chain. In this study, isoelectric-point-precipitation, heat-coagulation, ammonium-sulfate precipitation, high-pressure-assisted isoelectric-point precipitation, and high-pressure-assisted heat coagulation methods were used to extract proteins from sugar beet leaves. A mass spectrometry-based proteomic approach was used for comprehensive protein characterization. The analyses yielded 817 proteins, the most comprehensive protein profile on sugar beet leaves to date. Although the total protein contents were comparable, there was a significant difference between the methods for low-abundance proteins. High-pressure-assisted methods showed elevated levels of proteins predominantly located in the chloroplast. Here we showed for the first time that the extraction/precipitation methods may result in different protein profiles that potentially affect the physical and nutritional properties of functional products.

Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture

The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.

Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm

Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), or red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SIGNIFICANCE: Understanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution labeling proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. These multi-wavelengths lights function in a complex signaling network, which provide major challenges in inference of wavelength-specific molecular processes that underly the plant response. Besides, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further compare the changes to one another, rather than comparing plants proteome to FL, is thus necessary to gain the clear insights to specific underlying biological pathways and their effect consequences in plant response. Here, we employed narrow wavelength LED lights in our design to eliminate the potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the associates of proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant physiological processes particularly because of the tremendous increase in the amount of identified proteins which outreach the other biological data.

The search for new herbicide mechanisms of action: Is there a 'holy grail'?

New herbicide modes of action (MOAs) are in great demand because of the burgeoning evolution of resistance of weeds to existing commercial herbicides. This need has been exacerbated by the almost complete lack of introduction of herbicides with new MOAs for almost 40 years. There are many highly phytotoxic compounds with MOAs not represented by commercial herbicides, but neither these compounds nor structural analogues have been developed as herbicides for a variety of reasons. Natural products provide knowledge of many MOAs that are not being utilized by commercial herbicides. Other means of identifying new herbicide targets are discussed, including pharmaceutical target sites and metabolomic and proteomic information, as well as the use of artificial intelligence and machine learning to predict herbicidal compounds with new MOAs. Information about several newly discovered herbicidal compounds with new MOAs is summarized. The currently increased efforts of both established companies and start-up companies are likely to result in herbicides with new MOAs that can be used in herbicide resistance management within the next decade. © 2021 Society of Chemical Industry.

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions

The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.

Mining the Wheat Grain Proteome

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).

Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica

Coffea arabica is one of the most important crops worldwide. In vitro culture is an alternative for achieving Coffea regeneration, propagation, conservation, genetic improvement, and genome editing. The aim of this work was to identify proteins involved in auxin homeostasis by isobaric tandem mass tag (TMT) and the synchronous precursor selection (SPS)-based MS3 technology on the Orbitrap Fusion™ Tribrid mass spectrometer™ in three types of biological materials corresponding to C. arabica: plantlet leaves, calli, and suspension cultures. Proteins included in the β-oxidation of indole butyric acid and in the signaling, transport, and conjugation of indole-3-acetic acid were identified, such as the indole butyric response (IBR), the auxin binding protein (ABP), the ATP-binding cassette transporters (ABC), the Gretchen-Hagen 3 proteins (GH3), and the indole-3-acetic-leucine-resistant proteins (ILR). A more significant accumulation of proteins involved in auxin homeostasis was found in the suspension cultures vs. the plantlet, followed by callus vs. plantlet and suspension culture vs. callus, suggesting important roles of these proteins in the cell differentiation process.

iTRAQ-based proteomic analysis provides insights into the molecular mechanisms of rice formyl tetrahydrofolate deformylase in salt response

A new molecular mechanism of tetrahydrofolate deformylase involved in the salt response presumably affects mitochondrial and chloroplast function by regulating energy metabolism and accumulation of reactive oxygen species. High salinity severely restrains plant growth and development, consequently leading to a reduction in grain yield. It is therefore critical to identify the components involved in plant salt resistance. In our previous study, we identified a rice leaf early-senescence mutant hpa1, which encodes a formyl tetrahydrofolate deformylase (Xiong et al. in Sci China Life Sci 64(5):720-738, 2021). Here, we report that HPA1 also plays a role in the salt response. To explore the molecular mechanism of HPA1 in salt resistance, we attempted to identify the differentially expressed proteins between wild type and hpa1 mutant for salinity treatment using an iTRAQ-based comparative protein quantification approach. A total of 4598 proteins were identified, of which 279 were significantly altered, including 177 up- and 102 down-regulated proteins. A functional analysis suggested that the 279 differentially expressed proteins are involved mainly in the regulation of oxidative phosphorylation, phenylpropanoid biosynthesis, photosynthesis, posttranslational modifications, protein turnover and energy metabolism. Moreover, a deficiency in HPA1 impaired chlorophyll metabolism and photosynthesis in chloroplasts and affected the electron flow of the electron transport chain in mitochondria. These changes led to abnormal energy metabolism and accumulation of reactive oxygen species, which may affect the permeability and integrity of cell membranes, leading to cell death. In addition, the results were verified by transcriptional or physiological experiments. Our results provide an insight into a new molecular mechanism of the tetrahydrofolate cycle protein formyl tetrahydrofolate deformylase, which is involved in the salt response, presumably by affecting mitochondrial and chloroplast function regulating energy metabolism and accumulation of reactive oxygen species under salt stress.

Quantitative proteomics reveals the mechanism of slightly acidic electrolyzed water-induced buckwheat sprouts growth and flavonoids enrichment

Previous work has demonstrated that slightly acidic electrolyzed water (SAEW) can promote growth and nutrient enrichment of buckwheat sprouts. In this study, iTRAQ-based quantitative proteomic analysis of SAEW-induced buckwheat sprouts was conducted to explore its mechanism of action. The results showed that 11, 10 and 14 differentially expressed proteins (DEPs) related to energy metabolism, oxidative stress and flavonoid biosynthesis accumulated upwards and downwards, respectively, in SAEW-treated buckwheat. Bioinformatics analysis revealed 118 GO categories were in relation to molecular function. In the SAEW group, a total of 9 DEPs (5 up-regulated) were mapped to 10 significantly enriched KEGG pathways. SAEW induced flavonoid enrichment by modulating zymoproteins (e.g. phenylalanine ammonialyase and flavonol synthase) in phenylpropanoid biosynthesis pathway. qRT-PCR results had consistency with abundance levels of their corresponding proteins. These findings are likely to reveal the molecular mechanisms underlying the biochemical enrichment of buckwheat sprouts by SAEW.

In Planta Nanosensors: Understanding Biocorona Formation for Functional Design

Climate change and population growth are straining agricultural output. To counter these changes and meet the growing demand for food and energy, the monitoring and engineering of crops are becoming increasingly necessary. Nanoparticle-based sensors have emerged in recent years as new tools to advance agricultural practices. As these nanoparticle-based sensors enter and travel through the complex biofluids within plants, biomolecules including proteins, metabolites, lipids, and carbohydrates adsorb onto the nanoparticle surfaces, forming a coating known as the "bio-corona". Understanding these nanoparticle-biomolecule interactions that govern nanosensor function in plants will be essential to successfully develop and translate nanoparticle-based sensors into broader agricultural practice.

Quantitative proteomics analysis reveals the response mechanism of peanut (Arachis hypogaea L.) to imbibitional chilling stress

Imbibitional chilling stress inhibits normal seed germination and seedling establishment and leads to large losses in peanut production. This is a major limiting factor when sowing peanut earlier and further north. To reveal the response mechanism of peanut to imbibitional chilling stress, a Tandem Mass Tag (TMT)-based quantitative proteomics analysis was conducted to identify differentially accumulated proteins (DAPs) under imbibitional chilling stress. Hormone profiling and transcriptional analysis were performed to confirm the proteomics data. Further seed priming analysis with exogenous cytokinins was conducted to validate the role of cytokinins in alleviating imbibitional chilling injury. A total of 5029 proteins were identified and quantified in all of the experimental groups. Among these, 104 proteins were DAPs as compared with the control. Enrichment analysis revealed that these DAPs were significant in various molecular functional and biological processes, especially for biosynthesis and metabolism of plant hormones. Hormone profiling and transcription analysis suggested that the reduced abundance of cytokinin oxidase may be caused by down-regulation of gene expression of the corresponding genes and leads to an elevated content of cytokinins under chilling stress. Seed priming analysis suggested that exogenous application of cytokinins may alleviate injury caused by imbibitional chilling. Our study provides a comprehensive proteomics analysis of peanut under imbibitional chilling stress, suggesting the role of plant hormones in the response mechanism. The results provide a better understanding of the imbibitional chilling stress response mechanism in peanut that will aid in peanut production.

Deciphering plant-microbe crosstalk through proteomics studies

Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.

Unravelling mesosulfuron-methyl phytotoxicity and metabolism-based herbicide resistance in Alopecurus aequalis: Insight into regulatory mechanisms using proteomics

Non-target-site based resistance (NTSR), a poorly understood multigenic trait, has evolved as the greatest threat to crop production worldwide, by endowing weed plants an unpredictable pattern of resistance to herbicides. Our recent work with multiple-herbicide-resistant shortawn foxtail (Alopecurus aequalis Sobol.) biotype has preliminary indicated that cytochrome P450s-involved enhanced rate of mesosulfuron-methyl metabolism may involve in the NTSR. Here by further determining the differences in glutathione S-transferase (GST) activity and uptake and metabolic rates of mesosulfuron between resistant (R) and susceptible (S) A. aequalis plants, and associating them with endogenous differently regulated proteins (DEPs) identified from combinational proteomics analyses, we provided direct evidences on the enhanced herbicide degradation in resistant plants. Subsequently, the physiological phenotypes of photosynthesis, chlorophyll fluorescence, and antioxidation were compared between R and S plants and linked with correlative DEPs, indicating a series of key pathways including solar energy capture, photosynthetic electron transport, redox homeostasis, carbon fixation, photorespiration, and reactive oxygen species scavenging in susceptible plants were broken or severely damaged by mesosulfuron stress. In comparison, resistant plants have evolved enhanced herbicide degradation to minimize the accumulation of mesosulfuron and protect the photosynthesis and ascorbate-glutathione cycle against the adverse effects of chemical injury, giving A. aequalis plants a NTSR phenotype. Additionally, three key proteins respectively annotated as esterase, GST, and glucosyltransferase were identified and enabled as potential transcriptional markers for quick diagnosing the metabolic mesosulfuron resistance in A. aequalis species.

Transketolase Is Identified as a Target of Herbicidal Substance α-Terthienyl by Proteomics

α-terthienyl is a natural phytotoxin isolated originally from Flaveria bidentis (L.) Kuntze. The bioassay presented here shows the strong herbicidal activity of α-terthienyl on Digitaria sanguinalis, Arabidopsis thaliana and Chlamydomonas reinhardtii. The α-terthienyl-induced response of A. thaliana at the protein level was analyzed at different times. Changes in the protein expression profiles were analyzed by two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry (LC-MS/MS) mass spectrometry. Sixteen protein spots were identified that showed reproducible changes in the expression of at least 2-fold when compared to the control. Among these 16 spots, three were up-regulated and 13 were down-regulated. The decreased expression of several proteins associated with energy production and carbon metabolism suggested that these processes were affected by α-terthienyl. To search for the candidate proteins in this screen, A. thaliana T-DNA mutants of the candidate proteins were used to test their susceptibility to α-terthienyl. Amongst the others, attkl1, a mutant of transketolase, exhibited a significantly lower sensitivity to α-terthienyl when hit compared with Col-0. Based on the identification of the proteins associated with the response to α-terthienyl by proteomics, a candidate target protein transketolase was identified.

Isobaric Tags for Relative and Absolute Quantitation Proteomic Analysis of Germinating Barley under Gibberellin and Abscisic Acid Treatments

The degradation of starch in barley grains is a primary step of beer production. The addition of an appropriate amount of gibberellin (GA) promotes the production of fermentable sugars, beneficial to the brewing industry. However, the response of proteomics in germinating barley to GA and abscisic acid (ABA) treatments is not thoroughly understood. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) proteomics analysis was performed to illustrate the change of proteins in Tibetan wild barley XZ72 and XZ95 under GA and ABA treatments during germination. XZ72 had more proteins upregulated than XZ95 under GA treatment, while under ABA treatments, XZ95 had more proteins upregulated than XZ72. Concerning the proteins involved in energy metabolism under GA treatment, XZ72 had more proteins upregulated than XZ95. Among the 174 proteins related to starch metabolism, 31 proteins related to starch hydrolysis, such as α-amylase, α-glucosidase, and β-fructofuranosidase, showed higher relative abundance in control and GA treatments in XZ72 than in XZ95. Analysis of correlation between proteins and metabolites indicated that higher hydrolase activity is beneficial for the accumulation of fermentable sugars during germination. On the other hand, 26 starch-synthesis-related proteins were upregulated in XZ95 under ABA treatment. It may be suggested that GA-induced proteins act as accelerators of starch degradation, while ABA-induced proteins inhibit starch degradation. The current results showed that XZ72 is highly capable of allocating the starch-hydrolyzing enzymes, which play important roles in starch breakdown.

Microfabricated tools for quantitative plant biology

The development of microfabricated devices that will provide high-throughput quantitative data and high resolution in a fast, repeatable and reproducible manner is essential for plant biology research.

Approaches to Characterize Organelle, Compartment, or Structure Purity

The function of subcellular structures is defined by their specific sets of proteins, making subcellular protein localization one of the most important topics in organelle research. To date, many organelle proteomics workflows involve the (partial) purification of the desired subcellular structure and the subsequent analysis of the proteome using tandem mass spectrometry (MS/MS). This chapter gives an overview of the methods that have been used to assay the purity and enrichment of subcellular structures, with an emphasis on quantitative proteomics using differently enriched subcellular fractions. We introduce large-scale-based criteria for assignment of proteins to subcellular structures and describe in detail the use of ¹⁵N metabolic labeling in moss to characterize plastid and mitochondrial proteomes.

Tuber proteome comparison of five potato varieties by principal component analysis

BACKGROUND

Data analysis of omics data should be performed by multivariate analysis such as principal component analysis (PCA). The way data are clustered in PCA is of major importance to develop some classification systems based on multivariate analysis, such as soft independent modeling of class analogy (SIMCA). In a previous study a one-class classifier based on SIMCA was built using microarray data from a set of potatoes. The PCA grouped the transcriptomic data according to varieties. The present work aimed to use PCA to verify the clustering of the proteomic profiles for the same potato varieties.

RESULTS

Proteomic profiles of five potato varieties (Biogold, Fontane, Innovator, Lady Rosetta and Maris Piper) were evaluated by two-dimensional gel electrophoresis (2-DE) performed on two immobilized pH gradient (IPG) strip lengths, 13 and 24 cm, both under pH range 4-7. For each strip length, two gels were prepared from each variety; in total there were ten gels per analysis. For 13 cm strips, 199-320 spots were detected per gel, and for 24 cm strips, 365-684 spots.

CONCLUSION

All four PCAs performed with these datasets presented clear grouping of samples according to the varieties. The data presented here showed that PCA was applicable for proteomic analysis of potato and was able to separate the samples by varieties. © 2016 Society of Chemical Industry.

Differential proteomic analysis of embryogenic lines in oil palm (Elaeis guineensis Jacq)

Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using mass spectrometric analysis. Twelve prominent protein spots were then characterised using real-time polymerase chain reaction to compare the mRNA expression and protein abundant profiles. Three proteins, namely triosephosphate isomerase, l-ascorbate peroxidase, and superoxide dismutase were identified to be potential biomarker candidates at both the protein abundant and mRNA expression levels.

BIOLOGICAL SIGNIFICANCE

In this study, proteomic analysis was used to identify abundant proteins from total protein extracts. PEG fractionation was used to reveal lower abundant proteins from both high and low proliferation embryogenic lines of oil palm samples in tissue culture. A total of 40 protein spots were found to be significant in abundance and the mRNA levels of 12 of these were assessed using real time PCR. Three proteins namely, triosephosphate isomerase, l-ascorbate peroxidase and superoxide dismutase were found to be concordant in their mRNA expression and protein abundance. Triosephosphate isomerase is a key enzyme in glycolysis. Both l-ascorbate peroxidase and superoxide dismutase play a role in anti-oxidative scavenging defense systems. These proteins have potential for use as biomarkers to screen for high and low embryogenic oil palm samples.

The Increasing Impact of Activity-Based Protein Profiling in Plant Science

The active proteome dictates plant physiology. Yet, active proteins are difficult to predict based on transcript or protein levels, because protein activities are regulated post-translationally in their microenvironments. Over the past 10 years, activity-based protein profiling (ABPP) is increasingly used in plant science. ABPP monitors the activities of hundreds of plant proteins using tagged chemical probes that react with the active site of proteins in a mechanism-dependent manner. Since labeling is covalent and irreversible, labeled proteins can be detected and identified on protein gels and by mass spectrometry using tagged fluorophores and/or biotin. Here, we discuss general concepts, approaches and practical considerations of ABPP, before we summarize the discoveries made using 40 validated probes representing 14 chemotypes that can monitor the active state of >4,500 plant proteins. These discoveries and new opportunities indicate that this emerging functional proteomic technology is a powerful discovery tool that will have an increasing impact on plant science.

Comparative Proteomic Analysis of Cultured Suspension Cells of the Halophyte Halogeton glomeratus by iTRAQ Provides Insights into Response Mechanisms to Salt Stress

Soil salinity severely threatens land use capability and crop yields worldwide. An analysis of the molecular mechanisms of salt tolerance in halophytes will contribute to the development of salt-tolerant crops. In this study, a combination of physiological characteristics and iTRAQ-based proteomic approaches was conducted to investigate the molecular mechanisms underlying the salt response of suspension cell cultures of halophytic Halogeton glomeratus. These cells showed halophytic growth responses comparable to those of the whole plant. In total, 97 up-regulated proteins and 192 down-regulated proteins were identified as common to both 200 and 400 mM NaCl concentration treatments. Such salinity responsive proteins were mainly involved in energy, carbohydrate metabolism, stress defense, protein metabolism, signal transduction, cell growth, and cytoskeleton metabolism. Effective regulatory protein expression related to energy, stress defense, and carbohydrate metabolism play important roles in the salt-tolerance of H. glomeratus suspension cell cultures. However, known proteins regulating Na(+) efflux from the cytoplasm and its compartmentalization into the vacuole did not change significantly under salinity stress suggesting our existing knowledge concerning Na(+) extrusion and compartmentalization in halophytes needs to be evaluated further. Such data are discussed in the context of our current understandings of the mechanisms involved in the salinity response of the halophyte, H. glomeratus.

Leaf proteome comparison of two GM common bean varieties and their non-GM counterparts by principal component analysis

BACKGROUND

A genetically modified (GM) common bean event, namely Embrapa 5.1, was approved for commercialization in Brazil. The present work aimed to use principal component analysis (PCA) to compare the proteomic profile of this GM common bean and its non-GM counterpart.

RESULTS

Seedlings from four Brazilian common bean varieties were grown under controlled environmental conditions. Leaf proteomic profiles were analyzed by two-dimensional gel electrophoresis (2DE). First, a comparison among 12 gels from four common bean varieties was performed by PCA using volume percentage of 198 matched spots, presented in all gels. The first two principal components (PC) accounted for 46.8% of total variation. Two groups were clearly separated by the first component: Pérola and GM Pérola from Pontal and GM Pontal. Secondly, another comparison among six gels from the same variety GM and its non-GM counterpart was performed by PCA; in this case it was possible to distinguish GM and non-GM.

CONCLUSION

Separation between leaf proteomic profile of GM common bean variety and its counterpart was observed only when they were compared in pairs. These results showed higher similarity between GM variety and its counterpart than between two common bean varieties. PCA is a useful tool to compare proteomes of GM and non-GM plant varieties.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO₃)₂ at 500 mg L^-1(Pb500) and 1000 mg L^-1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included "cell wall," "apoplast," "response to metal ion," "vacuole," and "peroxidase activity," and the critical enriched pathways were involved in "citric acid (TCA) cycle and respiratory electron transport," "pyruvate metabolism," "phenylalanine metabolism," "phenylpropanoid biosynthesis," and "carbon metabolism." Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)-glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.

Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights

Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics.

Quantitative proteomics analysis reveals that S-nitrosoglutathione reductase (GSNOR) and nitric oxide signaling enhance poplar defense against chilling stress

NO acts as the essential signal to enhance poplar tolerance to chilling stress via antioxidant enzyme activities and protein S -nitrosylation modification, NO signal is also strictly controlled by S -nitrosoglutathione reductase and nitrate reductase to avoid the over-accumulation of reactive nitrogen species. Poplar (Populus trichocarpa) are fast growing woody plants with both ecological and economic value; however, the mechanisms by which poplar adapts to environmental stress are poorly understood. In this study, we used isobaric tags for relative and absolute quantification proteomic approach to characterize the response of poplar exposed to cold stress. We identified 114 proteins that were differentially expressed in plants exposed to cold stress. In particular, some of the proteins are involved in reactive oxygen species (ROS) and reactive nitrogen species (RNS) metabolism. Further physiological analysis showed that nitric oxide (NO) signaling activated a series of downstream defense responses. We further demonstrated that NO activated antioxidant enzyme activities and S-nitrosoglutathione reductase (GSNOR) activities, which would reduce ROS and RNS toxicity and thereby enhance poplar tolerance to cold stress. Suppressing NO accumulation or GSNOR activity aggravated cold damage to poplar leaves. Moreover, our results showed that RNS can suppress the activities of GSNOR and NO nitrate reductase (NR) by S-nitrosylation to fine-tune the NO signal and modulate ROS levels by modulating the S-nitrosylation of ascorbate peroxidase protein. Hence, our data demonstrate that NO signaling activates multiple pathways that enhance poplar tolerances to cold stress, and that NO signaling is strictly controlled through protein post-translational modification by S-nitrosylation.

Impairment in Sulfite Reductase Leads to Early Leaf Senescence in Tomato Plants

Sulfite reductase (SiR) is an essential enzyme of the sulfate assimilation reductive pathway, which catalyzes the reduction of sulfite to sulfide. Here, we show that tomato (Solanum lycopersicum) plants with impaired SiR expression due to RNA interference (SIR Ri) developed early leaf senescence. The visual chlorophyll degradation in leaves of SIR Ri mutants was accompanied by a reduction of maximal quantum yield, as well as accumulation of hydrogen peroxide and malondialdehyde, a product of lipid peroxidation. Interestingly, messenger RNA transcripts and proteins involved in chlorophyll breakdown in the chloroplasts were found to be enhanced in the mutants, while transcripts and their plastidic proteins, functioning in photosystem II, were reduced in these mutants compared with wild-type leaves. As a consequence of SiR impairment, the levels of sulfite, sulfate, and thiosulfate were higher and glutathione levels were lower compared with the wild type. Unexpectedly, in a futile attempt to compensate for the low glutathione, the activity of adenosine-5'-phosphosulfate reductase was enhanced, leading to further sulfite accumulation in SIR Ri plants. Increased sulfite oxidation to sulfate and incorporation of sulfite into sulfoquinovosyl diacylglycerols were not sufficient to maintain low basal sulfite levels, resulting in accumulative leaf damage in mutant leaves. Our results indicate that, in addition to its biosynthetic role, SiR plays an important role in prevention of premature senescence. The higher sulfite is likely the main reason for the initiation of chlorophyll degradation, while the lower glutathione as well as the higher hydrogen peroxide and malondialdehyde additionally contribute to premature senescence in mutant leaves.

The membrane proteome of Medicago truncatula roots displays qualitative and quantitative changes in response to arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis that associates roots of most land plants with soil-borne fungi (Glomeromycota), is characterized by reciprocal nutritional benefits. Fungal colonization of plant roots induces massive changes in cortical cells where the fungus differentiates an arbuscule, which drives proliferation of the plasma membrane. Despite the recognized importance of membrane proteins in sustaining AM symbiosis, the root microsomal proteome elicited upon mycorrhiza still remains to be explored. In this study, we first examined the qualitative composition of the root membrane proteome of Medicago truncatula after microsome enrichment and subsequent in depth analysis by GeLC-MS/MS. The results obtained highlighted the identification of 1226 root membrane protein candidates whose cellular and functional classifications predispose plastids and protein synthesis as prevalent organelle and function, respectively. Changes at the protein abundance level between the membrane proteomes of mycorrhizal and nonmycorrhizal roots were further monitored by spectral counting, which retrieved a total of 96 proteins that displayed a differential accumulation upon AM symbiosis. Besides the canonical markers of the periarbuscular membrane, new candidates supporting the importance of membrane trafficking events during mycorrhiza establishment/functioning were identified, including flotillin-like proteins. The data have been deposited to the ProteomeXchange with identifier PXD000875.

BIOLOGICAL SIGNIFICANCE

During arbuscular mycorrhizal symbiosis, one of the most widespread mutualistic associations in nature, the endomembrane system of plant roots is believed to undergo qualitative and quantitative changes in order to sustain both the accommodation process of the AM fungus within cortical cells and the exchange of nutrients between symbionts. Large-scale GeLC-MS/MS proteomic analysis of the membrane fractions from mycorrhizal and nonmycorrhizal roots of M. truncatula coupled to spectral counting retrieved around one hundred proteins that displayed changes in abundance upon mycorrhizal establishment. The symbiosis-related membrane proteins that were identified mostly function in signaling/membrane trafficking and nutrient uptake regulation. Besides extending the coverage of the root membrane proteome of M. truncatula, new candidates involved in the symbiotic program emerged from the current study, which pointed out a dynamic reorganization of microsomal proteins during the accommodation of AM fungi within cortical cells.

The link between transcript regulation and de novo protein synthesis in the retrograde high light acclimation response of Arabidopsis thaliana

Background

Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumulation and de novo protein synthesis. While signalling cues, transcriptomes and some involved players have been characterized, an integrated view is only slowly emerging, and information on the translational level is missing. Transfer of low (8 μmol quanta^.m^-2.s^-1) or normal light (80 μmol quanta^.m^-2.s^-1) acclimated 30 d old Arabidopsis thaliana plants to high light (800 μmol quanta^.m^-2.s^-1) triggers retrograde signals. Using this established approach, we sought to link transcriptome data with de novo synthesized proteins by in vivo labelling with ³⁵S methionine and proteome composition.

Results

De novo synthesized protein and proteome patterns could reliably be matched with newly annotated master gels. Each molecular level could be quantified for a set of 41 proteins. Among the proteins preferentially synthesized in plants transferred to high light were enzymes including carbonic anhydrase, fructose-1,6-bisphosphate aldolase, O-acetyl serine thiol lyase, and chaperones, while low rates upon transfer to high light were measured for e.g. dehydroascorbate reductase, glyceraldehyde-3-phosphate dehydrogenase and CuZn superoxide dismutase, and opposite responses between 10-fold and 100-fold light increment for e.g. glutamine synthetase and phosphoglycerate kinase.

Conclusions

The results prove the hypothesis that transcript abundance is poorly linked to de novo protein synthesis due to profound regulation at the level of translation. This vertical systems biology approach enables to quantitatively and kinetically link the molecular levels for scrutinizing signal processing and response generation.

Root proteome of rice studied by iTRAQ provides integrated insight into aluminum stress tolerance mechanisms in plants

One of the major limitations to crop growth on acid soils is the prevalence of soluble aluminum ions (Al(3+)). Rice (Oryza sativa L.) has been reported to be highly Al tolerant; however, large-scale proteomic data of rice in response to Al(3+) are still very scanty. Here, we used an iTRAQ-based quantitative proteomics approach for comparative analysis of the expression profiles of proteins in rice roots in response to Al(3+) at an early phase. A total of 700 distinct proteins (homologous proteins grouped together) with >95% confidence were identified. Among them, 106 proteins were differentially expressed upon Al(3+) toxicity in sensitive and tolerant cultivars. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was the most significantly up-regulated biochemical process in response to excess Al(3+). The mRNA levels of eight proteins mapped in the glycolysis/gluconeogenesis were further analyzed by qPCR and the expression levels of all the eight genes were higher in tolerant cultivar than in sensitive cultivar, suggesting that these compounds may promote Al tolerance by modulating the production of available energy. Although the exact roles of these putative tolerance proteins remain to be examined, our data lead to a better understanding of the Al tolerance mechanisms in rice plants through the proteomics approach.

BIOLOGICAL SIGNIFICANCE

Aluminum (mainly Al(3+)) is one of the major limitations to the agricultural productivity on acid soils and causes heavy yield loss every year. Rice has been reported to be highly Al tolerant; however, the mechanisms of rice Al tolerance are still not fully understood. Here, a combined proteomics, bioinformatics and qPCR analysis revealed that Al(3+) invasion caused complex proteomic changes in rice roots involving energy, stress and defense, protein turnover, metabolism, signal transduction, transport and intracellular traffic, cell structure, cell growth/division, and transcription. Promotion of the glycolytic/gluconeogenetic pathway in roots appeared crucially important for Al tolerance. These results lead to a better understanding of the Al tolerance mechanisms in rice and help to improve plant performance on acid soils, eventually to increase the crop production.

Uncovering plant-pathogen crosstalk through apoplastic proteomic studies

Plant pathogens have evolved by developing different strategies to infect their host, which in turn have elaborated immune responses to counter the pathogen invasion. The apoplast, including the cell wall and extracellular space outside the plasma membrane, is one of the first compartments where pathogen-host interaction occurs. The plant cell wall is composed of a complex network of polysaccharides polymers and glycoproteins and serves as a natural physical barrier against pathogen invasion. The apoplastic fluid, circulating through the cell wall and intercellular spaces, provides a means for delivering molecules and facilitating intercellular communications. Some plant-pathogen interactions lead to plant cell wall degradation allowing pathogens to penetrate into the cells. In turn, the plant immune system recognizes microbial- or damage-associated molecular patterns (MAMPs or DAMPs) and initiates a set of basal immune responses, including the strengthening of the plant cell wall. The establishment of defense requires the regulation of a wide variety of proteins that are involved at different levels, from receptor perception of the pathogen via signaling mechanisms to the strengthening of the cell wall or degradation of the pathogen itself. A fine regulation of apoplastic proteins is therefore essential for rapid and effective pathogen perception and for maintaining cell wall integrity. This review aims to provide insight into analyses using proteomic approaches of the apoplast to highlight the modulation of the apoplastic protein patterns during pathogen infection and to unravel the key players involved in plant-pathogen interaction.

Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome

We report here a systematic evaluation of a multiplex mass spectrometry method coupled with ion mobility separation (HD-MS(E)) for the identification and quantification of proteins in the chloroplast stroma. We show that this method allows the robust quantification of reference proteins in mixtures, and it detects concentration differences with high sensitivity when three replicas are performed. Applied to the analysis of the chloroplast stroma proteome, HD-MS(E) identified and quantified many chloroplast proteins that were not previously identified in large-scale proteome analyses, suggesting HD-MS(E) as a suitable complementary tool for discovery proteomics. We find that HD-MS(E) tends to underestimate protein abundances at concentrations above 25fmol, which is likely due to ion transmission loss and detector saturation. This limitation can be circumvented by omitting the ion mobility separation step in the HD-MS(E) workflow. The robustness of protein quantification is influenced by the selection of peptides and their intensity distribution, therefore critical scrutiny of quantification results is required. Based on the HD-MS(E) quantification of chloroplast stroma proteins we performed a meta-analysis and compared published quantitative data with our results, using a parts per million normalization scheme. Important pathways in the chloroplast stroma show quantitative stability against different experimental conditions and quantification strategies.

BIOLOGICAL SIGNIFICANCE

Our analysis establishes MS(E)-based Hi3 quantification as a tool for the absolute quantification of proteins in the chloroplast stroma. The meta-analysis performed with a parts per million normalization scheme shows that quantitative proteomics data acquired in different labs and with different quantification strategies yield comparable results for some metabolic pathways, while others show a higher variability. Our data therefore indicate that such meta-analyses allow distinguishing robust from fine-controlled metabolic pathways.

Proteomics in deciphering the auxin commitment in the Arabidopsis thaliana root growth

The development of plant root systems is characterized by a high plasticity, made possible by the continual propagation of new meristems. Root architecture is fundamental for overall plant growth, abiotic stress resistance, nutrient uptake, and response to environmental changes. Understanding the function of genes and proteins that control root architecture and stress resistance will contribute to the development of more sustainable systems of intensified crop production. To meet these challenges, proteomics provide the genome-wide scale characterization of protein expression pattern, subcellular localization, post-translational modifications, activity regulation, and molecular interactions. In this review, we describe a variety of proteomic strategies that have been applied to study the proteome of the whole organ and of specific cell types during root development. Each has advantages and limitations, but collectively they are providing important insights into the mechanisms by which auxin structures and patterns the root system and into the interplay between signaling networks, auxin transport and growth. The acquisition of proteomic, transcriptomic, and metabolomic data sets of the root apex on the cell scale has revealed the high spatial complexity of regulatory networks and fosters the use of new powerful proteomic tools for a full understanding of the control of root developmental processes and environmental responses.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

Coping with abiotic stress: proteome changes for crop improvement

Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade

Non-target-site-based resistance (NTSR) can confer unpredictable cross-resistance to herbicides. However, the genetic determinants of NTSR remain poorly known. The current, urgent challenge for weed scientists is thus to elucidate the bases of NTSR so that detection tools are developed, the evolution of NTSR is understood, the efficacy of the shrinking herbicide portfolio is maintained and integrated weed management strategies, including fully effective herbicide applications, are designed and implemented. In this paper, the importance of NTSR in resistance to herbicides is underlined. The most likely way in which NTSR evolves-by accumulation of different mechanisms within individual plants-is described. The NTSR mechanisms, which can interfere with herbicide penetration, translocation and accumulation at the target site, and/or protect the plant against the consequences of herbicide action, are then reviewed. NTSR is a part of the plant stress response. As such, NTSR is a dynamic process unrolling over time that involves 'protectors' directly interfering with herbicide action, and also regulators controlling 'protector' expression. NTSR is thus a quantitative trait. On this basis, a three-step procedure is proposed, based on the use of the 'omics' (genomics, transcriptomics, proteomics or metabolomics), to unravel the genetic bases of NTSR.

Omics methods for probing the mode of action of natural and synthetic phytotoxins

For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

Deep profiling of the transcriptome and proteome during leaf development reveals unexpected responses to water deficit, as well as a surprising lack of protein-level fluctuations during the day–night cycle, despite clear changes at the transcript level.

Transcript and protein variation patterns reflect the functional stages of the leaf.

Protein and transcript levels correlate well during leaf development, with some notable exceptions.

Diurnal transcript-level fluctuations are not matched by corresponding diurnal fluctuations in the detected proteome.

Continuous reduced soil water content results in reduced leaf growth, but the plant adapts at molecular levels without showing a typical drought response.

Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water conditions. We found that the lower soil water potential led to reduced, but prolonged, growth and an adaptation at the molecular level without a drought stress response. Clustering of the protein and transcript data using a decision tree revealed different patterns in abundance changes across the growth stages and between end-of-day and end-of-night that are linked to specific biological functions. Correlations between protein and transcript levels depend on the time-of-day and also on protein localisation and function. Surprisingly, only very few of >1700 quantified proteins showed diurnal abundance fluctuations, despite strong fluctuations at the transcript level.

Predictive models for transient protein expression in tobacco (Nicotiana tabacum L.) can optimize process time, yield, and downstream costs

The transient expression of recombinant biopharmaceutical proteins in plants can suffer inter-batch variation, which is considered a major drawback under the strict regulatory demands imposed by current good manufacturing practice (cGMP). However, we have achieved transient expression of the monoclonal antibody 2G12 and the fluorescent marker protein DsRed in tobacco leaves with ∼ 15% intra-batch coefficients of variation, which is within the range reported for transgenic plants. We developed models for the transient expression of both proteins that predicted quantitative expression levels based on five parameters: The OD(600 nm) of Agrobacterium tumefaciens (from 0.13 to 2.00), post-inoculation incubation temperature (15-30°C), plant age (harvest at 40 or 47 days after seeding), leaf age, and position within the leaf. The expression models were combined with a model of plant biomass distribution and extraction, generating a yield model for each target protein that could predict the amount of protein in specific leaf parts, individual leaves, groups of leaves, and whole plants. When the yield model was combined with a cost function for the production process, we were able to perform calculations to optimize process time, yield, or downstream costs. We illustrate this procedure by transferring the cost function from a production process using transgenic plants to a hypothetical process for the transient expression of 2G12. Our models allow the economic evaluation of new plant-based production processes and provide greater insight into the parameters that affect transient protein expression in plants.

Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges - A review

The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.

Performance of isobaric and isotopic labeling in quantitative plant proteomics

Mass spectrometry has become indispensable for peptide and protein quantification in proteomics studies. When proteomics technologies are applied to understand the biology of plants, two-dimensional gel electrophoresis is still the prevalent method for protein fractionation, identification, and quantitation. In the present work, we have used LC-MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical labeling technique to quantify proteins in the endosperm of Ricinus communis seeds at three developmental stages (IV, VI, and X). Endosperm proteins of each stage were trypsin-digested in-solution, and the same amount of peptides was labeled with ICPL and iTRAQ tags in two orders (forward and reverse). Each sample was submitted to nanoLC coupled to an LTQ-Orbitrap high-resolution mass spectrometer. Comparing labeling performance, iTRAQ was able to label 99.8% of all identified unique peptides, while 94.1% were labeled by ICPL. After statistical analysis, it was possible to quantify 309 (ICPL) and 321 (iTRAQ) proteins, from which 95 are specific to ICPL, 107 to iTRAQ, and 214 common to both labeling strategies. We noted that the iTRAQ quantification could be influenced by the tag. Even though the efficiency of the iTRAQ and ICPL in protein quantification depends on several parameters, both labeling methods were able to successfully quantify proteins present in the endosperm of castor bean during seed development and, when combined, increase the number of quantified proteins.