Study of Early Leaf Senescence in Arabidopsis thaliana by Quantitative Proteomics Using Reciprocal 14N/15N Labeling and Difference Gel Electrophoresis

Function of Protein Kinases in Leaf Senescence of Plants

Leaf senescence is an evolutionarily acquired process and it is critical for plant fitness. During senescence, macromolecules and nutrients are disassembled and relocated to actively growing organs. Plant leaf senescence process can be triggered by developmental cues and environmental factors, proper regulation of this process is essential to improve crop yield. Protein kinases are enzymes that modify their substrates activities by changing the conformation, stability, and localization of those proteins, to play a crucial role in the leaf senescence process. Impressive progress has been made in understanding the role of different protein kinases in leaf senescence recently. This review focuses on the recent progresses in plant leaf senescence-related kinases. We summarize the current understanding of the function of kinases on senescence signal perception and transduction, to help us better understand how the orderly senescence degeneration process is regulated by kinases, and how the kinase functions in the intricate integration of environmental signals and leaf age information.

SILIA-Based 4C Quantitative PTM Proteomics

To absolutely and relatively quantitate the alteration of a posttranslationally modified (PTM) proteome in response to a specific internal or external signal, a ¹⁵N-stable isotope labeling in Arabidopsis (SILIA) protocol has been integrated into the 4C quantitative PTM proteomics, named as SILIA-based 4C quantitative PTM proteomics (S4Quap). The isotope metabolic labeling produces both forward (F) and reciprocal (R) mixings of either ¹⁴N/¹⁵N-coded tissues or the ¹⁴N/¹⁵N-coded total cellular proteins. Plant protein is isolated using a urea-based extraction buffer (UEB). The presence of 8 M urea, 2% polyvinylpolypyrrolidone (PVPP), and 5 mM ascorbic acid allows to instantly denature protein, remove the phenolic compounds, and curb the oxidation by free radicals once plant cells are broken. The total cellular proteins are routinely processed into peptides by trypsin. The PTM peptide yield of affinity enrichment and preparation is 0.1-0.2% in general. Ion exchange chromatographic fractionation prepares the PTM peptides for LC-MS/MS analysis. The collected mass spectrograms are subjected to a target-decoy sequence analysis using various search engines. The computational programs are subsequently applied to analyze the ratios of the extracted ion chromatogram (XIC) of the ¹⁴N/¹⁵N isotope-coded PTM peptide ions and to perform the statistical evaluation of the quantitation results. The Student t-test values of ratios of quantifiable ¹⁴N/¹⁵N-coded PTM peptides are normally corrected using a Benjamini-Hochberg (BH) multiple hypothesis test to select the significantly regulated PTM peptide groups (BH-FDR < 5%). Consequently, the highly selected prospect candidate(s) of PTM proteins are confirmed and validated using biochemical, molecular, cellular, and transgenic plant analysis.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Proteomic and Biochemical Changes during Senescence of Phalaenopsis 'Red Dragon' Petals

Phalaenopsis flowers are some of the most popular ornamental flowers in the world. For most ornamental plants, petal longevity determines postharvest quality and garden performance. Therefore, it is important to have insight into the senescence mechanism of Phalaenopsis. In the present study, a proteomic approach combined with ultrastructural observation and activity analysis of antioxidant enzymes was used to profile the molecular and biochemical changes during pollination-induced petal senescence in Phalaenopsis “Red Dragon”. Petals appeared to be visibly wilting at 24 h after pollination, accompanied by the mass degradation of macromolecules and organelles during senescence. In addition, 48 protein spots with significant differences in abundance were found by two-dimensional electrophoresis (2-DE) and subjected to matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS). There were 42 protein spots successfully identified and homologous to known functional protein species involved in key biological processes, including antioxidant pathways, stress response, protein metabolism, cell wall component metabolism, energy metabolism, cell structure, and signal transduction. The activity of all reactive oxygen species (ROS)-scavenging enzymes was increased, keeping the content of ROS at a low level at the early stage of senescence. These results suggest that two processes, a counteraction against increased levels of ROS and the degradation of cellular constituents for maintaining nutrient recycling, are activated during pollination-induced petal senescence in Phalaenopsis. The information provides a basis for understanding the mechanism regulating petal senescence and prolonging the florescence of Phalaenopsis.

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants

The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.

Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition

Quantitative proteomics strategies - which are playing important roles in the expanding field of plant molecular systems biology - are traditionally designated as either hypothesis driven or non-hypothesis driven. Many of these strategies aim to select individual peptide ions for tandem mass spectrometry (MS/MS), and to do this mixed hypothesis driven and non-hypothesis driven approaches are theoretically simple to implement. In-depth investigations into the efficacies of such approaches have, however, yet to be described. In this study, using combined samples of unlabeled and metabolically ¹⁵N-labeled Arabidopsis thaliana proteins, we investigate the mixed use of targeted data acquisition (TDA) and data dependent acquisition (DDA) - referred to as TDA/DDA - to facilitate both hypothesis driven and non-hypothesis driven quantitative data collection in individual LC-MS/MS experiments. To investigate TDA/DDA for hypothesis driven data collection, 7 miRNA target proteins of differing size and abundance were targeted using inclusion lists comprised of 1558 m/z values, using 3 different TDA/DDA experimental designs. In samples in which targeted peptide ions were of particularly low abundance (i.e., predominantly only marginally above mass analyser detection limits), TDA/DDA produced statistically significant increases in the number of targeted peptides identified (230 ± 8 versus 80 ± 3 for DDA; p = 1.1 × 10^-3) and quantified (35 ± 3 versus 21 ± 2 for DDA; p = 0.038) per experiment relative to the use of DDA only. These expected improvements in hypothesis driven data collection were observed alongside unexpected improvements in non-hypothesis driven data collection. Untargeted peptide ions with m/z values matching those in inclusion lists were repeatedly identified and quantified across technical replicate TDA/DDA experiments, resulting in significant increases in the percentages of proteins repeatedly quantified in TDA/DDA experiments only relative to DDA experiments only (33.0 ± 2.6% versus 8.0 ± 2.7%, respectively; p = 0.011). These results were observed together with uncompromised broad-scale MS/MS data collection in TDA/DDA experiments relative to DDA experiments. Using our observations we provide guidelines for TDA/DDA method design for quantitative plant proteomics studies, and suggest that TDA/DDA is a broadly underutilized proteomics data acquisition strategy.

Coupling of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deep into the leaf senescence proteome of Glycine max

Leaf senescence is the last stage of leaf development that re-mobilizes nutrients from the source to sink. Here, we have utilized the soybean as a model system to unravel senescence-associated proteins (SAPs). A comparative proteomics approach was used at two contrasting stages of leaf development, namely mature (R3) and senescent (R7). Selection criteria for these two stages were the contrasting differences in their biochemical parameters - chlorophyll, carotenoids and malondialdehyde contents. Proteome analysis involved subjecting the total leaf proteins to 15% poly-ethylene glycol (PEG) pre-fractional method to enrich the low-abundance proteins (LAPs) and their analyses by gel-based 2-DE and 1-DE shotgun proteomics approaches. 2-DE profiling of PEG-supernatant and -pellet fractions detected 153 differential spots between R3 and R7 stages, of which 102 proteins were identified. In parallel, 1-DE shotgun proteomics approach identified 598 and 534 proteins in supernatant and pellet fractions of R3 and R7 stages, respectively. MapMan and Gene Ontology analyses showed increased abundance and/or specific accumulation of proteins related to jasmonic acid biosynthesis and defense, while proteins associated with photosynthesis and ROS-detoxification were decreased during leaf senescence. These findings and the generated datasets further our understanding on leaf senescence at protein level, providing a resource for the scientific community.

BIOLOGICAL SIGNIFICANCE

Leaf senescence is a major biological event in the life cycle of plants that leads to the recycling of nutrients. However, the molecular mechanisms underlying leaf senescence still remain poorly understood. Here, we used a combination of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deeper into the leaf senescence proteome using soybean leaf as a model experimental material. For the identification of low-abundance proteins, polyethylene glycol (PEG) fractionation was employed and both PEG-supernatant and -pellet fractions were utilized for 2-DE and shotgun proteomic analysis. A total of 1234 (102 from 2-DE and 1132 from 1-DE shotgun proteome analysis) proteins were identified which were functionally annotated using GO and MapMan bioinformatics tools. Our results also emphasize the role of jasmonic acid in soybean leaf senescence.

Can stable isotope mass spectrometry replace ‎radiolabelled approaches in metabolic studies?

Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.

Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research

Leaf senescence is a complex but tightly regulated developmental process involving a coordinated sequence of multiple molecular events, which ultimately leads to death of the leaf. Efforts to understand the mechanistic principles underlying leaf senescence have been largely made by transcriptomic, proteomic, and metabolomic studies over the past decade. This review focuses on recent milestones in leaf senescence research obtained using multi-omics technologies, as well as future endeavors toward systems understanding of leaf senescence processes. In particular, we discuss recent advances in understanding molecular events during leaf senescence through genome-wide transcriptome analyses in Arabidopsis. We also describe comparative transcriptome analyses used to unveil the commonality and diversity of regulatory mechanisms governing leaf senescence in the plant kingdom. Finally, we provide current illustrations of epigenomic, proteomic, and metabolomic landscapes of leaf senescence. We envisage that integration of multi-omics leaf senescence data will enable us to address unresolved questions regarding leaf senescence, including determining the molecular principles that coordinate concurrent and ordered changes in biological events during leaf senescence.

Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula

Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought acclimation as well as a more thorough understanding of the molecular mechanisms of stress recovery. Plants are exposed to a continuously changing environment. Extremes such as several weeks of drought are followed by rain. This requires a molecular plasticity of the plant enabling drought acclimation and the necessity of deacclimation processes for recovery and continuous growth.

During drought stress and subsequent recovery, the metabolome and proteome are regulated through a sequence of molecular processes including synthesis and degradation and molecular interaction networks are part of this regulatory process. In order to study this complex regulatory network, a comprehensive analysis is presented for the first time, investigating protein turnover and regulatory classes of proteins and metabolites during a stress recovery scenario in the model legume Medicago truncatula. The data give novel insights into the molecular capacity and differential processes required for acclimation and deacclimation of severe drought stressed plants.

Functional cluster and network analyses unraveled independent regulatory mechanisms for stress and recovery with different dynamic phases that during the course of recovery define the plants deacclimation from stress. The combination of relative abundance levels and turnover analysis revealed an early transition phase that seems key for recovery initiation through water resupply and is independent from renutrition. Thus, a first indication for a metabolite and protein-based load capacity was observed necessary for the recovery from drought, an important but thus far ignored possible feature toward tolerance. The data indicate that apart from the plants molecular stress response mechanisms, plasticity may be related to the nutritional status of the plant prior to stress initiation. A new perspective and possible new targets as well as metabolic mechanisms for future plant-bioengineering toward enhanced drought stress tolerance are presented.

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Sulfite Oxidase Activity Is Essential for Normal Sulfur, Nitrogen and Carbon Metabolism in Tomato Leaves

Plant sulfite oxidase [SO; E.C.1.8.3.1] has been shown to be a key player in protecting plants against exogenous toxic sulfite. Recently we showed that SO activity is essential to cope with rising dark-induced endogenous sulfite levels in tomato plants (Lycopersicon esculentum/Solanum lycopersicum Mill. cv. Rheinlands Ruhm). Here we uncover the ramifications of SO impairment on carbon, nitrogen and sulfur (S) metabolites. Current analysis of the wild-type and SO-impaired plants revealed that under controlled conditions, the imbalanced sulfite level resulting from SO impairment conferred a metabolic shift towards elevated reduced S-compounds, namely sulfide, S-amino acids (S-AA), Co-A and acetyl-CoA, followed by non-S-AA, nitrogen and carbon metabolite enhancement, including polar lipids. Exposing plants to dark-induced carbon starvation resulted in a higher degradation of S-compounds, total AA, carbohydrates, polar lipids and total RNA in the mutant plants. Significantly, a failure to balance the carbon backbones was evident in the mutants, indicated by an increase in tricarboxylic acid cycle (TCA) cycle intermediates, whereas a decrease was shown in stressed wild-type plants. These results indicate that the role of SO is not limited to a rescue reaction under elevated sulfite, but SO is a key player in maintaining optimal carbon, nitrogen and sulfur metabolism in tomato plants.

The role of nitrogen in leaf senescence of summer maize and analysis of underlying mechanisms using comparative proteomics

Leaf senescence is associated with fundamental changes on the level of the proteome and it can be modulated by nitrogen. To determine the precise regulatory mechanisms underlying these effects, we conducted a comparative proteomics study using 2-dimensional gel electrophoresis and MALDI-TOF/TOF MS. Based on our study of the maize leaf proteome, leaf senescence induces complex responses including the degradation of 32 senescence-associated proteins that are involved in many biological processes, especially energy, metabolism and cell rescue, defense and virulence pathways. Although similar conclusions have been highlighted in other crops, this study filled the knowledge gap in maize leaf senescence. Moreover, we discovered, for the first time, 29 "nitrogen-regulated senescence proteins" had significant (P≤0.05) interaction term for nitrogen×stage. Although further study of nitrogen-related senescence proteins, such as 30S ribosomal protein, will be required to fully elucidate their complex functions, the surprising results in our study provide a new vision to research the relationship between nitrogen and senescence.

Proteomic analysis of residual proteins in blades and petioles of fallen leaves of Brassica napus

Brassica napus L. is an important crop plant, characterised by high nitrogen (N) levels in fallen leaves, leading to a significant restitution of this element to the soil, with important consequences at the economic and environmental levels. It is now well established that the N in fallen leaves is due to weak N remobilisation that is especially related to incomplete degradation of foliar proteins during leaf senescence. Identification of residual proteins in a fallen leaf (i.e. incompletely degraded in the last step of the N remobilisation process) constitutes important information for improving nutrient use efficiency. Proteome analysis of the vascular system (petioles) and blades from fallen leaves of Brassica napus was performed, and the 30 most abundant residual proteins in each tissue were identified. Among them, several proteins involved in N recycling remain in the leaf after abscission. Moreover, this study reveals that some residual proteins are associated with energy metabolism, protection against oxidative stress, and more surprisingly, photosynthesis. Finally, comparison of blade and petiole proteomes show that, despite their different physiological roles in the non-senescing leaf, both organs redirect their metabolism in order to ensure catabolic reactions. Taken together, the results suggest that a better degradation of these leaf proteins during the senescence process could enable improvements in the N use efficiency of Brassica napus.

Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data

Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover.

An in-advance stable isotope labeling strategy for relative analysis of multiple acidic plant hormones in sub-milligram Arabidopsis thaliana seedling and a single seed

A sensitive and reliable in-advance stable isotope labeling strategy was developed for simultaneous relative quantification of 8 acidic plant hormones in sub-milligram amount of plant materials. Bromocholine bromide (BETA) and its deuterated counterpart D9-BETA were used to in-advance derivatize control and sample extracts individually, which were then combined and subjected to solid-phase extraction (SPE) purification followed by UPLC-MS/MS analysis. Relative quantification of target compounds was obtained by calculation of the peak area ratios of BETA/D9-BETA labeled plant hormones. The in-advance stable isotope labeling strategy realized internal standard-based relative quantification of multiple kinds of plant hormones independent of availability of internal standard of every analyte with enhanced sensitivity of 1-3 orders of magnitude. Meanwhile, the in-advance labeling contributes to higher sample throughput and more reliability. The method was successfully applied to determine 8 plant hormones in 0.8mg DW (dry weight) of seedlings and 4 plant hormones from single seed of Arabidopsis thaliana. The results show the potential of the method in relative quantification of multiple plant hormones in tiny plant tissues or organs, which will advance the knowledge of the crosstalk mechanism of plant hormones.

SILAC and alternatives in studying cellular proteomes of plants

Quantitative proteomics by metabolic labeling has a high impact on the growing field of plant systems biology. SILAC has been pioneered and optimized for plant cell culture systems allowing for SILAC-based quantitative experiments in specialized experimental setups. In comparison to other model organisms, the application of SILAC to whole plants is challenging. As autotrophic organisms, plants under their natural growth conditions can hardly be fully labeled with stable isotope-coded amino acids. The metabolic labeling with inorganic nitrogen is therefore the method of choice for most whole-plant physiological questions. Plants can easily metabolize different inorganic nitrogen isotopes. The incorporation of the labeled inorganic nitrogen then results in proteins and metabolites with distinct molecular mass, which can be detected on a mass spectrometer. In comparative quantitative experiments, similarly as in SILAC experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches were developed for metabolite identification. Here we present a typical hydroponics setup, the workflow for processing of samples, mass spectrometry and data analysis for large-scale metabolic labeling experiments of whole plants.

Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics

Stable Isotope Labelling by Amino acids in Cell culture (SILAC) is a powerful technique for comparative quantitative proteomics, which has recently been applied to a number of different eukaryotic organisms. Inefficient incorporation of labelled amino acids in cell cultures of Arabidopsis thaliana has led to very limited use of SILAC in plant systems. We present a method allowing, for the first time, efficient labelling with stable isotope-containing arginine and lysine of whole Arabidopsis seedlings. To illustrate the utility of this method, we have combined the high labelling efficiency (>95%) with quantitative proteomics analyses of seedlings exposed to increased salt concentration. In plants treated for 7 days with 80 mM NaCl, a relatively mild salt stress, 215 proteins were identified whose expression levels changed significantly compared to untreated seedling controls. The 92 up-regulated proteins included proteins involved in abiotic stress responses and photosynthesis, while the 123 down-regulated proteins were enriched in proteins involved in reduction of oxidative stress and other stress responses, respectively. Efficient labelling of whole Arabidopsis seedlings by this modified SILAC method opens new opportunities to exploit the genetic resources of Arabidopsis and analyse the impact of mutations on quantitative protein dynamics in vivo.

Towards systems biological understanding of leaf senescence

The application of systems biology approaches has greatly facilitated the process of deciphering the molecular mechanisms underlying leaf senescence. Analyses of the leaf senescence transcriptome have identified some of the major biochemical events during senescence including protein degradation and nutrient remobilization. Proteomic studies have confirmed these findings and have suggested up-regulated energy metabolism during leaf senescence which might be important for cell viability maintenance. As a critical part of systems biology, studies involving transcription regulation networking and senescence-inducing signaling have deepened our understanding on the molecular regulation of leaf senescence. The important next steps towards a systems biological understanding of leaf senescence will be discussed.

Proteomics and transcriptomics of broccoli subjected to exogenously supplied and transgenic senescence-induced cytokinin for amelioration of postharvest yellowing

Previously, we investigated transgenic broccoli harboring senescence-associated-gene (SAG) promoter-triggered isopentenyltransferase (ipt), which encodes the key enzyme for cytokinin (CK) synthesis and mimics the action of exogenous supplied CK in delaying postharvest senescence of broccoli. Here, we used proteomics and transcriptomics to compare the mechanisms of ipt-transgenic and N(6)-benzylaminopurine (BA) CK treatment of broccoli during postharvest storage. The 2 treatments conferred common and distinct mechanisms. BA treatment decreased the quantity of proteins involved in energy and carbohydrate metabolism and amino acid metabolism, and ipt-transgenic treatment increased that of stress-related proteins and molecular chaperones and slightly affected levels of carbohydrate metabolism proteins. Both treatments regulated genes involved in CK signaling, sugar transport, energy and carbohydrate metabolism, amino acid metabolism and lipid metabolism, although ipt-transgenic treatment to a lesser extent. BA treatment induced genes encoding molecular chaperones, whereas ipt-transgenic treatment induced stress-related genes for cellular protection during storage. Both BA and ipt-transgenic treatments acted antagonistically on ethylene functions. We propose a long-term acclimation of metabolism and protection systems with ipt-transgenic treatment of broccoli and short-term modulation of metabolism and establishment of a protection system with both BA and ipt-transgenic treatments in delaying senescence of broccoli florets.

BIOLOGICAL SIGNIFICANCE

Transgenic broccoli harboring senescence-associated-gene (SAG) promoter-triggered isopentenyltransferase (ipt), which encodes the key enzyme for cytokinin (CK) synthesis and N(6)-benzylaminopurine (BA) CK treated broccoli both showed retardation of postharvest senescence during storage. The mechanisms underlying the two treatments were compared. The combination of proteomic and transcriptomic evidences revealed that the 2 treatments conferred common and distinct mechanisms in delaying senescence of broccoli florets. We propose a long-term acclimation of metabolism and protection systems with ipt-transgenic treatment of broccoli and short-term modulation of metabolism and establishment of a protection system with both BA and ipt-transgenic treatments in delaying senescence of broccoli florets. This article is part of a Special Issue entitled: Translational Plant Proteomics.

RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula

An intron-spliced hairpin RNA approach was used for the targeted silencing of the MtTdp1α gene encoding the αisoform of tyrosyl-DNA phosphodiesterase 1 in Medicago truncatula Gaertn. Tyrosyl-DNA phosphodiesterase 1, involved in the repair of DNA topoisomerase I-mediated DNA damage, has been poorly investigated in plants. RNA-Seq analysis, carried out in the MtTdp1α-depleted plants, revealed different levels of transcriptional modulation (up- and down-regulation, alternative splicing, activation of alternative promoter) in genes involved in DNA damage sensing, DNA repair, and chromatin remodelling. It is suggested that the MtTdp1α gene has new, previously undetected roles in maintaining genome integrity. Up-regulation of senescence-associated genes and telomere shortening were observed. Moreover, impaired ribosome biogenesis indicated that the MtTdp1α gene is required for the nucleolar function. In agreement with the RNA-Seq data, transmission electron microscopy detected an altered nucleolar architecture in the MtTdp1α-depleted cells. Based on the reported data, a working hypothesis related to the occurrence of a nucleolar checkpoint in plant cells is proposed.

An essential role for tomato sulfite oxidase and enzymes of the sulfite network in maintaining leaf sulfite homeostasis

Little is known about the homeostasis of sulfite levels, a cytotoxic by-product of plant sulfur turnover. By employing extended dark to induce catabolic pathways, we followed key elements of the sulfite network enzymes that include adenosine-5'-phosphosulfate reductase and the sulfite scavengers sulfite oxidase (SO), sulfite reductase, UDP-sulfoquinovose synthase, and β-mercaptopyruvate sulfurtransferases. During extended dark, SO was enhanced in tomato (Solanum lycopersicum) wild-type leaves, while the other sulfite network components were down-regulated. SO RNA interference plants lacking SO activity accumulated sulfite, resulting in leaf damage and mortality. Exogenous sulfite application induced up-regulation of the sulfite scavenger activities in dark-stressed or unstressed wild-type plants, while expression of the sulfite producer, adenosine-5'-phosphosulfate reductase, was down-regulated. Unstressed or dark-stressed wild-type plants were resistant to sulfite applications, but SO RNA interference plants showed sensitivity and overaccumulation of sulfite. Hence, under extended dark stress, SO activity is necessary to cope with rising endogenous sulfite levels. However, under nonstressed conditions, the sulfite network can control sulfite levels in the absence of SO activity. The novel evidence provided by the synchronous dark-induced turnover of sulfur-containing compounds, augmented by exogenous sulfite applications, underlines the role of SO and other sulfite network components in maintaining sulfite homeostasis, where sulfite appears to act as an orchestrating signal molecule.

Find pairs: the module for protein quantification of the PeakQuant software suite

Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data. For demonstrating the high applicability of FindPairs, we focused on the quantitative analysis of proteome data acquired in (14)N/(15)N labeling experiments. We further provide a comprehensive overview of the features of the FindPairs software, and compare these with existing quantification packages. The software presented here supports a wide range of proteomics applications, allowing one to quantitatively assess data derived from different stable isotope labeling approaches, such as (14)N/(15)N labeling, SILAC, and iTRAQ. The software is publicly available at http://www.medizinisches-proteom-center.de/software and free for academic use.

The use of heavy nitrogen in quantitative proteomics experiments in plants

In the growing field of plant systems biology, there is an undisputed need for methods allowing accurate quantitation of proteins and metabolites. As autotrophic organisms, plants can easily metabolize different nitrogen isotopes, resulting in proteins and metabolites with distinct molecular mass that can be separated on a mass spectrometer. In comparative quantitative experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches have been developed for metabolite identification. Here, we present an overview of currently used experimental strategies in heavy nitrogen labeling in plants and provide background on the history and function of this quantitation technique.

Application of proteomics in the mechanistic study of traditional Chinese medicine

Systems biology is considered to be the possible technology that could bring breakthroughs in the study of TCM (traditional Chinese medicine). Proteomics, as one of the major components of systems biology, has been used in the mechanistic study of TCM, providing some interesting results. In the present paper, we review the current application of proteomics in the mechanistic study of TCM. Proteomics technologies and strategies that might be used in the future to improve study of TCM are also discussed.

Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots

The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a (15)N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (K(S)) and degradation (K(D)) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify K(S) and K(D) for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. K(S) and K(D) correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive (15)N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability.

Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics

Hydroponic isotope labeling of entire plants (HILEP) combines hydroponic plant cultivation and metabolic labeling with stable isotopes using (15)N-containing inorganic salts to label whole and mature plants. Employing (15)N salts as the sole nitrogen source for HILEP leads to the production of healthy-looking plants which contain (15)N proteins labeled to nearly 100%. Therefore, HILEP is suitable for quantitative plant proteomic analysis, where plants are grown in either (14)N- or (15)N-hydroponic media and pooled when the biological samples are collected for relative proteome quantitation. The pooled (14)N-/(15)N-protein extracts can be fractionated in any suitable way and digested with a protease for shotgun proteomics, using typically reverse phase liquid chromatography nanoelectrospray ionization tandem mass spectrometry (RPLC-nESI-MS/MS). Best results were obtained with a hybrid ion trap/FT-MS mass spectrometer, combining high mass accuracy and sensitivity for the MS data acquisition with speed and high-throughput MS/MS data acquisition, increasing the number of proteins identified and quantified and improving protein quantitation. Peak processing and picking from raw MS data files, protein identification, and quantitation were performed in a highly automated way using integrated MS data analysis software with minimum manual intervention, thus easing the analytical workflow. In this methodology paper, we describe how to grow Arabidopsis plants hydroponically for isotope labeling using (15)N salts and how to quantitate the resulting proteomes using a convenient workflow that does not require extensive bioinformatics skills.

Plant organelle proteomics: collaborating for optimal cell function

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.

Advances in qualitative and quantitative plant membrane proteomics

The membrane proteome consists of integral and membrane-associated proteins that are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are only expressed during certain developmental stages or in response to environmental stress. These proteins can undergo post-translational modifications in response to these different conditions, allowing them to transiently associate with the membrane or other membrane proteins. Along with their increased size, hydrophobicity, and the additional organelle and cellular features of plant cells relative to mammalian systems, the characterization of the plant membrane proteome presents unique challenges for effective qualitative and quantitative analysis using mass spectrometry (MS) analysis. Here, we present the latest advancements developed for the isolation and fractionation of plant organelles and their membrane components amenable to MS analysis. Separations of membrane proteins from these enriched preparations that have proven effective are discussed for both gel- and liquid chromatography-based MS analysis. In this context, quantitative membrane proteomic analyses using both isotope-coded and label-free approaches are presented and reveal the potential to establish a wider-biological interpretation of the function of plant membrane proteins that will ultimately lead to a more comprehensive understanding of plant physiology and their response mechanisms.

Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA)

In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated.

Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane

Gluconacetobacter diazotrophicus is a plant-growth-promoting bacterium that colonizes sugarcane. In order to investigate molecular aspects of the G. diazotrophicus-sugarcane interaction, we performed a quantitative mass spectrometry-based proteomic analysis by (15)N metabolic labeling of bacteria, root samples, and co-cultures. Overall, more than 400 proteins were analyzed and 78 were differentially expressed between the plant-bacterium interaction model and control cultures. A comparative analysis of the G. diazotrophicus in interaction with two distinct genotypes of sugarcane, SP70-1143 and Chunee, revealed proteins with fundamental roles in cellular recognition. G. diazotrophicus presented proteins involved in adaptation to atypical conditions and signaling systems during the interaction with both genotypes. However, SP70-1143 and Chunee, sugarcane genotypes with high and low contribution of biological nitrogen fixation, showed divergent responses in contact with G. diazotrophicus. The SP70-1143 genotype overexpressed proteins from signaling cascades and one from a lipid metabolism pathway, whereas Chunee differentially synthesized proteins involved in chromatin remodeling and protein degradation pathways. In addition, we have identified 30 bacterial proteins in the roots of the plant samples; from those, nine were specifically induced by plant signals. This is the first quantitative proteomic analysis of a bacterium-plant interaction, which generated insights into early signaling of the G. diazotrophicus-sugarcane interaction.

Toward a definition of the complete proteome of plant peroxisomes: Where experimental proteomics must be complemented by bioinformatics

In the past few years, proteome analysis of Arabidopsis peroxisomes has been established by the complementary efforts of four research groups and has emerged as the major unbiased approach to identify new peroxisomal proteins on a large scale. Collectively, more than 100 new candidate proteins from plant peroxisomes have been identified, including long-awaited low-abundance proteins. More than 50 proteins have been validated as peroxisome targeted, nearly doubling the number of established plant peroxisomal proteins. Sequence homologies of the new proteins predict unexpected enzyme activities, novel metabolic pathways and unknown non-metabolic peroxisome functions. Despite this remarkable success, proteome analyses of plant peroxisomes remain highly material intensive and require major preparative efforts. Characterization of the membrane proteome or post-translational protein modifications poses major technical challenges. New strategies, including quantitative mass spectrometry methods, need to be applied to allow further identifications of plant peroxisomal proteins, such as of stress-inducible proteins. In the long process of defining the complete proteome of plant peroxisomes, the prediction of peroxisome-targeted proteins from plant genome sequences emerges as an essential complementary approach to identify additional peroxisomal proteins that are, for instance, specific to peroxisome variants from minor tissues and organs or to abiotically stressed model and crop plants.

A proteomic approach towards the identification of the matrix protein content of the two types of microbodies in Neurospora crassa

Microbodies (peroxisomes) comprise a class of organelles with a similar biogenesis but remarkable biochemical heterogeneity. Here, we purified the two distinct microbody family members of filamentous fungi, glyoxysomes and Woronin bodies, from Neurospora crassa and analyzed their protein content by HPLC/ESI-MS/MS. In the purified Woronin bodies, we unambiguously identified only hexagonal 1 (HEX1), suggesting that the matrix is probably exclusively filled with the HEX1 hexagonal crystal. The proteomic analysis of highly purified glyoxysomes allowed the identification of 191 proteins. Among them were 16 proteins with a peroxisomal targeting signal type 1 (PTS1) and three with a PTS2. The collection also contained the previously described N. crassa glyoxysomal matrix proteins FOX2 and ICL1 that lack a typical PTS. Three PTS1 proteins were identified that likely represent the long sought glyoxysomal acyl-CoA dehydrogenases of filamentous fungi. Two of them were demonstrated by subcellular localization studies to be indeed glyoxysomal. Furthermore, two PTS proteins were identified that are suggested to be involved in the detoxification of nitroalkanes. Since the glyoxysomal localization was experimentally demonstrated for one of these enzymes, a new biochemical reaction is expected to be associated with microbody function.

A reciprocal 15N-labeling proteomic analysis of expanding Arabidopsis leaves subjected to osmotic stress indicates importance of mitochondria in preserving plastid functions

Plants respond to environmental stress by dynamically reprogramming their growth. Whereas stress onset is accompanied by rapid growth inhibition leading to smaller organs, growth will recover and adapt once the stress conditions become stable and do no threaten plant survival. Here, adaptation of growing Arabidopsis thaliana leaves to mild and prolonged osmotic stress was investigated by means of a complete metabolic labeling strategy with the (15)N-stable isotope as a complement to a previously published transcript and metabolite profiling. Global analysis of protein changes revealed that plastidial ATPase, Calvin cycle, and photorespiration were down-regulated, but mitochondrial ATP synthesis was up-regulated, indicating the importance of mitochondria in preserving plastid functions during water stress. Although transcript and protein data correlated well with the stable and prolonged character of the applied stress, numerous proteins were clearly regulated at the post-transcriptional level that could, at least partly, be related to changes in protein synthesis and degradation. In conclusion, proteomics using the (15)N labeling helped understand the mechanisms underlying growth adaptation to osmotic stress and allowed the identification of candidate genes to improve plant growth under limited water.

Quantitative measurement of phosphopeptides and proteins via stable isotope labeling in Arabidopsis and functional phosphoproteomic strategies

Protein phosphorylation is one type of posttranslational modification, which regulates a large number of cellular processes in plant cells. As an emerging powerful biotechnology that integrates all aspects of advantages from mass spectrometry, bioinformatics, and genomics, phosphoproteomics offers us an unprecedented high-throughput methodology with high sensitivity and dashing speed in identifying a large complement of phosphoproteins from plant cells within a relatively short period of time. Needless to say, phosphoproteomics has become an integral portion of life sciences, which penetrates various research disciplines of biology, agriculture, and forestry and irreversibly changes the way by which plant scientists study biological problems.Because phosphorylation/dephosphorylation of protein is dynamic in cells and the amount of phosphoproteins is low, the preservation of a phosphor group onto phosphosite throughout protein purification as well as enrichment of these phosphoproteins during purification has become a serious technical issue. To overcome difficulties commonly associated with phosphoprotein isolation, phosphopeptides' enrichment, and mass spectrometry analysis, we have developed a urea-based phosphoprotein purification protocol for plants, which instantly denatures plant proteins once the total cell content comes into contact with the UEB solution. To measure the alteration of phosphorylation on a phosphosite using mass spectrometer, an in vivo (15)N metabolic labeling method (SILIA, i.e., stable isotope labeling in Arabidopsis) has been developed and applied for Arabidopsis differential phosphoproteomics. Thus far, hundreds of signaling-specific phosphoproteins have been identified using both label-free and (15)N-labeled differential phosphoproteomic approach. The phosphoproteomics has allowed us to identify a number of signaling components mediating plant cell signaling in Arabidopsis. It is envisaged that a huge number of phosphosites will continue to be uncovered from phosphoproteomics in the near future, which will become instrumental for the development of plant phosphor-relay networks and molecular systems biology.

Peptide and protein quantification: a map of the minefield

The increasing popularity of gel-free proteomics technologies has created a strong demand for compatible quantitative analysis methods. As a result, a plethora of different techniques has been proposed to perform gel-free quantitative analysis of proteomics samples. Each of these methods comes with certain strengths and shortcomings, and they often are dedicated to a specific purpose. This review will present a brief overview of the main methods, organized by their underlying concepts, and will discuss the issues they raise with a focus on data processing. Finally, we will list the available software that can help with the data processing from quantitative experiments. We hope that this review will thus enable researchers to find the most appropriate method available for their research objectives, and can also serve as a basis for creating a reliable data processing strategy.

Proteomic analysis of pollination-induced corolla senescence in petunia

Senescence represents the last phase of petal development during which macromolecules and organelles are degraded and nutrients are recycled to developing tissues. To understand better the post-transcriptional changes regulating petal senescence, a proteomic approach was used to profile protein changes during the senescence of Petuniaxhybrida 'Mitchell Diploid' corollas. Total soluble proteins were extracted from unpollinated petunia corollas at 0, 24, 48, and 72 h after flower opening and at 24, 48, and 72 h after pollination. Two-dimensional gel electrophoresis (2-DE) was used to identify proteins that were differentially expressed in non-senescing (unpollinated) and senescing (pollinated) corollas, and image analysis was used to determine which proteins were up- or down-regulated by the experimentally determined cut-off of 2.1-fold for P <0.05. One hundred and thirty-three differentially expressed protein spots were selected for sequencing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine the identity of these proteins. Searching translated EST databases and the NCBI non-redundant protein database, it was possible to assign a putative identification to greater than 90% of these proteins. Many of the senescence up-regulated proteins were putatively involved in defence and stress responses or macromolecule catabolism. Some proteins, not previously characterized during flower senescence, were identified, including an orthologue of the tomato abscisic acid stress ripening protein 4 (ASR4). Gene expression patterns did not always correlate with protein expression, confirming that both proteomic and genomic approaches will be required to obtain a detailed understanding of the regulation of petal senescence.

Quantitation in mass-spectrometry-based proteomics

Mass-spectrometry-based proteomics, the large-scale analysis of proteins by mass spectrometry, has emerged as a new technology over the last decade and become routine in many plant biology laboratories. While early work consisted merely of listing proteins identified in a given organ or under different conditions of interest, there is a growing need to apply comparative and quantitative proteomics strategies toward gaining novel insights into functional aspects of plant proteins and their dynamics. However, during the transition from qualitative to quantitative protein analysis, the potential and challenges will be tightly coupled. Several strategies for differential proteomics that involve stable isotopes or label-free comparisons and their statistical assessment are possible, each having specific strengths and limitations. Furthermore, incomplete proteome coverage and restricted dynamic range still impose the strongest limitations to data throughput and precise quantitative analysis. This review gives an overview of the current state of the art in differential proteomics and possible strategies in data processing.

Quantitative proteomics by metabolic labeling of model organisms

In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life.

Proteomics of the response of Arabidopsis thaliana to infection with Alternaria brassicicola

We have studied the proteome of the model plant Arabidopsis thaliana infected with a necrotrophic fungal pathogen, Alternaria brassicicola. The Arabidopsis-A. brassicicola host-pathogen pair is being developed as a model genetic system for incompatible plant-fungal interactions, in which the spread of disease is limited by plant defense responses. After confirming that a defense response was induced at the transcriptional level, we identified proteins whose abundance on 2-DE gels increased or decreased in infected leaves. At least 11 protein spots showed reproducible differences in abundance, increasing or decreasing during the progress of the infection. The pathogenesis-related protein PR4, a glycosyl hydrolase, and the antifungal protein osmotin are strongly up-regulated. Two members of the Arabidopsis glutathione S-transferase (GST) family increased in abundance in infected leaves. The spots in which these GST proteins were identified contain additional members of the GST family. Representation of GST family members in several protein spots migrating at similar molecular weight suggests post-translational modifications. The signature of GST regulation may be specific for the type of plant-pathogen interaction. The proteomic view of the defense response to A. brassicicola can be compared with other types of plant-pathogen interactions, and to leaf senescence, identifying unique regulatory patterns.