Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit

Regulation of invertase activity in different root zones of wheat (Triticum aestivum L.) seedlings in the course of osmotic adjustment under water deficit conditions

Osmotic adjustment of roots is an essential adaptive mechanism to sustain water uptake and root growth under water deficit. In this paper, the role of invertases (β-fructofuranosidase, EC 3.2.1.26) in osmotic adjustment was investigated in the root tips (cell division and elongation zone) and the root maturation zone of wheat (Triticum aestivum L. cv. Josef) in the course of osmotic stress imposed by 20% polyethylene glycol (PEG) 6000. The two root zones investigated differed distinctly in the response of invertases to water deprivation. In the root tips, the activity of the vacuolar and cell wall-bound invertases increased markedly under water stress resulting in the accumulation of hexoses (glucose and fructose) that contributed significantly to osmotic adjustment. A transient rise in hydrogen peroxide (H2O2) preceded the enhancement of invertases upon exposure to osmotic stress. Treatment with the NADPH oxidase inhibitor diphenylene iodonium (DPI) abolished the stress induced H2O2 production and suppressed the stimulation of the vacuolar invertase activity, whereas the activity of the cell wall-bound invertase was not influenced by DPI. As a consequence of the inhibitory effect of DPI on the vacuolar invertase, hexose levels and osmotic adjustment were also markedly decreased in the root tips under water deficit in the presence of DPI. These data suggest that H2O2 probably generated by a NADPH oxidase is required as a signalling molecule for the up-regulation of the vacuolar invertase activity in the root tips under osmotic stress, thereby enhancing the capacity for osmotic adjustment. In the root maturation zone, an early H2O2 signal could not be detected in response to PEG application. Only an increase in the glucose level that was not paralleled by fructose and a slight stimulation of the activity of the vacuolar invertase occurred in the maturation zone after water deprivation. The stress induced accumulation of glucose in the maturation zone was not affected by DPI and thus seems to be not regulated by NADPH oxidase-derived H2O2. Altogether, osmotic adjustment was considerably smaller in the maturation zone than in the root tips.

Differential expression of α-L-arabinofuranosidases during maize (Zea mays L.) root elongation

Specific α- l -arabinofuranosidases are involved in the realisation of elongation growth process in cells with type II cell walls. Elongation growth in a plant cell is largely based on modification of the cell wall. In type II cell walls, the Ara/Xyl ratio is known to decrease during elongation due to the partial removal of Ara residues from glucuronoarabinoxylan. We searched within the maize genome for the genes of all predicted α-L-arabinofuranosidases that may be responsible for such a process and related their expression to the activity of the enzyme and the amount of free arabinose measured in six zones of a growing maize root. Eight genes of the GH51 family (ZmaABFs) and one gene of the GH3 family (ZmaARA-I) were identified. The abundance of ZmaABF1 and 3-6 transcripts was highly correlated with the measured enzymatic activity and free arabinose content that significantly increased during elongation. The transcript abundances also coincided with the pattern of changes in the Ara/Xyl ratio of the xylanase-extractable glucuronoarabinoxylan described in previous studies. The expression of ZmaABF3, 5 and 6 was especially up-regulated during elongation although corresponding proteins are devoid of the catalytic glutamate at the proper position. ZmaABF2 transcripts were specifically enriched in the root cap and meristem. A single ZmaARA-I gene was not expressed as a whole gene but instead as splice variants that encode the C-terminal end of the protein. Changes in the ZmaARA-I transcript level were rather moderate and had no significant correlation with free arabinose content. Thus, elongation growth of cells with type II cell walls is accompanied by the up-regulation of specific and predicted α-L-arabinofuranosidase genes, and the corresponding activity is indeed pronounced and is important for the modification of glucuronoarabinoxylan, which plays a key role in the modification of the cell wall supramolecular organisation.

A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes

A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.

Cell wall proteomic of Brachypodium distachyon grains: A focus on cell wall remodeling proteins

Cell walls play key roles during plant development. Following their deposition into the cell wall, polysaccharides are continually remodeled according to the growth stage and stress environment to accommodate cell growth and differentiation. To date, little is known concerning the enzymes involved in cell wall remodeling, especially in gramineous and particularly in the grain during development. Here, we investigated the cell wall proteome of the grain of Brachypodium distachyon. This plant is a suitable model for temperate cereal crops. Among the 601 proteins identified, 299 were predicted to be secreted. These proteins were distributed into eight functional classes; the class of proteins that act on carbohydrates was the most highly represented. Among these proteins, numerous glycoside hydrolases were found. Expansins and peroxidases, which are assumed to be involved in cell wall polysaccharide remodeling, were also identified. Approximately half of the proteins identified in this study were newly discovered in grain and were not identified in the previous proteome analysis conducted using the culms and leaves of B. distachyon. Therefore, the data obtained from all organs of B. distachyon infer a global cell wall proteome consisting of 460 proteins. At present, this is the most extensive cell wall proteome of a monocot species.

The divining root: moisture-driven responses of roots at the micro- and macro-scale

Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.

Modelling the coordination of the controls of stomatal aperture, transpiration, leaf growth, and abscisic acid: update and extension of the Tardieu-Davies model

Stomatal aperture, transpiration, leaf growth, hydraulic conductance, and concentration of abscisic acid in the xylem sap ([ABA]xyl) vary rapidly with time of day. They follow deterministic relations with environmental conditions and interact in such a way that a change in any one of them affects all the others. Hence, approaches based on measurements of one variable at a given time or on paired correlations are prone to a confusion of effects, in particular for studying their genetic variability. A dynamic model allows the simulation of environmental effects on the variables, and of multiple feedbacks between them at varying time resolutions. This paper reviews the control of water movement through the plant, stomatal aperture and growth, and translates them into equations in a model. It includes recent progress in understanding the intrinsic and environmental controls of tissue hydraulic conductance as a function of transpiration rate, circadian rhythms, and [ABA]xyl. Measured leaf water potential is considered as the water potential of a capacitance representing mature tissues, which reacts more slowly to environmental cues than xylem water potential and expansive growth. Combined with equations for water and ABA fluxes, it results in a dynamic model able to simulate variables with genotype-specific parameters. It allows adaptive roles for hydraulic processes to be proposed, in particular the circadian oscillation of root hydraulic conductance. The script of the model, in the R language, is included together with appropriate documentation and examples.

The divining root: moisture-driven responses of roots at the micro- and macro-scale

Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.

Down-regulation of ZmEXPB6 (Zea mays β-expansin 6) protein is correlated with salt-mediated growth reduction in the leaves of Z. mays L

The salt-sensitive crop Zea mays L. shows a rapid leaf growth reduction upon NaCl stress. There is increasing evidence that salinity impairs the ability of the cell walls to expand, ultimately inhibiting growth. Wall-loosening is a prerequisite for cell wall expansion, a process that is under the control of cell wall-located expansin proteins. In this study the abundance of those proteins was analyzed against salt stress using gel-based two-dimensional proteomics and two-dimensional Western blotting. Results show that ZmEXPB6 (Z. mays β-expansin 6) protein is lacking in growth-inhibited leaves of salt-stressed maize. Of note, the exogenous application of heterologously expressed and metal-chelate-affinity chromatography-purified ZmEXPB6 on growth-reduced leaves that lack native ZmEXPB6 under NaCl stress partially restored leaf growth. In vitro assays on frozen-thawed leaf sections revealed that recombinant ZmEXPB6 acts on the capacity of the walls to extend. Our results identify expansins as a factor that partially restores leaf growth of maize in saline environments.

Protein turnover in plant biology

The protein content of plant cells is constantly being updated. This process is driven by the opposing actions of protein degradation, which defines the half-life of each polypeptide, and protein synthesis. Our understanding of the processes that regulate protein synthesis and degradation in plants has advanced significantly over the past decade. Post-transcriptional modifications that influence features of the mRNA populations, such as poly(A) tail length and secondary structure, contribute to the regulation of protein synthesis. Post-translational modifications such as phosphorylation, ubiquitination and non-enzymatic processes such as nitrosylation and carbonylation, govern the rate of degradation. Regulators such as the plant TOR kinase, and effectors such as the E3 ligases, allow plants to balance protein synthesis and degradation under developmental and environmental change. Establishing an integrated understanding of the processes that underpin changes in protein abundance under various physiological and developmental scenarios will accelerate our ability to model and rationally engineer plants.

Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

BACKGROUND

Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.

RESULTS

Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.

CONCLUSION

Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.

Cell Wall Metabolism in Response to Abiotic Stress

This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions.

Physiological and proteomic adaptation of the alpine grass Stipa purpurea to a drought gradient

Stipa purpurea, an endemic forage species on the Tibetan Plateau, is highly resistant to cold and drought, but the mechanisms underlying its responses to drought stress remain elusive. An understanding of such mechanisms may be useful for developing cultivars that are adaptable to water deficit. In this study, we analyzed the physiological and proteomic responses of S. purpurea under increasing drought stress. Seedlings of S. purpurea were subjected to a drought gradient in a controlled experiment, and proteins showing changes in abundance under these conditions were identified by two-dimensional electrophoresis followed by mass spectrometry analysis. A western blotting analysis was conducted to confirm the increased abundance of a heat-shock protein, NCED2, and a dehydrin in S. purpurea seedlings under drought conditions. We detected carbonylated proteins to identify oxidation-sensitive proteins in S. purpurea seedlings, and found that ribulose-1, 5-bisphosphate carboxylase oxygenase (RuBisCO) was one of the oxidation-sensitive proteins under drought. Together, these results indicated drought stress might inhibit photosynthesis in S. purpurea by oxidizing RuBisCO, but the plants were able to maintain photosynthetic efficiency by a compensatory upregulation of unoxidized RuBisCO and other photosynthesis-related proteins. Further analyses confirmed that increased abundance of antioxidant enzymes could balance the redox status of the plants to mitigate drought-induced oxidative damage.

Advances in plant proteomics toward improvement of crop productivity and stress resistancex

Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.

Transcriptomic complexity in young maize primary roots in response to low water potentials

BACKGROUND

Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding of the molecular mechanisms underlying the water deficit response of crops will enable targeted breeding strategies to develop robust cultivars.

RESULTS

In the present study, the transcriptional response of maize (Zea mays L.) primary roots to low water potentials was monitored by RNA sequencing (RNA-Seq) experiments. After 6 h and 24 h of mild (-0.2 MPa) and severe (-0.8 MPa) water deficit conditions, the primary root transcriptomes of seedlings grown under water deficit and control conditions were compared. The number of responsive genes was dependent on and increased with intensification of water deficit treatment. After short-term mild and severe water deficit 249 and 3,000 genes were differentially expressed, respectively. After a 24 h treatment the number of affected genes increased to 7,267 and 12,838 for mild and severe water deficit, respectively, including more than 80% of the short-term responsive genes. About half of the differentially expressed genes were up-regulated and maximal fold-changes increased with treatment intensity to more than 300-fold. A consensus set of 53 genes was differentially regulated independently of the nature of deficit treatment. Characterization revealed an overrepresentation of the Gene Ontology (GO) categories "oxidoreductase activity" and "heme binding" among regulated genes connecting the water deficit response to ROS metabolism.

CONCLUSION

This study gives a comprehensive insight in water deficit responsive genes in young maize primary roots and provides a set of candidate genes that merit further genetic analyses in the future.

Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways?

Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components.

A hydraulic model is compatible with rapid changes in leaf elongation under fluctuating evaporative demand and soil water status

Plants are constantly facing rapid changes in evaporative demand and soil water content, which affect their water status and growth. In apparent contradiction to a hydraulic hypothesis, leaf elongation rate (LER) declined in the morning and recovered upon soil rehydration considerably quicker than transpiration rate and leaf water potential (typical half-times of 30 min versus 1-2 h). The morning decline of LER began at very low light and transpiration and closely followed the stomatal opening of leaves receiving direct light, which represent a small fraction of leaf area. A simulation model in maize (Zea mays) suggests that these findings are still compatible with a hydraulic hypothesis. The small water flux linked to stomatal aperture would be sufficient to decrease water potentials of the xylem and growing tissues, thereby causing a rapid decline of simulated LER, while the simulated water potential of mature tissues declines more slowly due to a high hydraulic capacitance. The model also captured growth patterns in the evening or upon soil rehydration. Changes in plant hydraulic conductance partly counteracted those of transpiration. Root hydraulic conductivity increased continuously in the morning, consistent with the transcript abundance of Zea maize Plasma Membrane Intrinsic Protein aquaporins. Transgenic lines underproducing abscisic acid, with lower hydraulic conductivity and higher stomatal conductance, had a LER declining more rapidly than wild-type plants. Whole-genome transcriptome and phosphoproteome analyses suggested that the hydraulic processes proposed here might be associated with other rapidly occurring mechanisms. Overall, the mechanisms and model presented here may be an essential component of drought tolerance in naturally fluctuating evaporative demand and soil moisture.

Genetic and physiological controls of growth under water deficit

The sensitivity of expansive growth to water deficit has a large genetic variability, which is higher than that of photosynthesis. It is observed in several species, with some genotypes stopping growth in a relatively wet soil, whereas others continue growing until the lower limit of soil-available water. The responses of growth to soil water deficit and evaporative demand share an appreciable part of their genetic control through the colocation of quantitative trait loci as do the responses of the growth of different organs to water deficit. This result may be caused by common mechanisms of action discussed in this paper (particularly, plant hydraulic properties). We propose that expansive growth, putatively linked to hydraulic processes, determines the sink strength under water deficit, whereas photosynthesis determines source strength. These findings have large consequences for plant modeling under water deficit and for the design of breeding programs.

Progress and challenges for abiotic stress proteomics of crop plants

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.

Cell wall remodeling under abiotic stress

Plants exposed to abiotic stress respond to unfavorable conditions on multiple levels. One challenge under drought stress is to reduce shoot growth while maintaining root growth, a process requiring differential cell wall synthesis and remodeling. Key players in this process are the formation of reactive oxygen species (ROS) and peroxidases, which initially cross-link phenolic compounds and glycoproteins of the cell walls causing stiffening. The function of ROS shifts after having converted all the peroxidase substrates in the cell wall. If ROS-levels remain high during prolonged stress, OH°-radicals are formed which lead to polymer cleavage. In concert with xyloglucan modifying enzymes and expansins, the resulting cell wall loosening allows further growth of stressed organs.

Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.)

Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure.

Abscisic acid- and stress-induced highly proline-rich glycoproteins regulate root growth in rice

In the root of rice (Oryza sativa), abscisic acid (ABA) treatment, salinity, or water deficit stress induces the expression of a family of four genes, REPETITIVE PROLINE-RICH PROTEIN (RePRP). These genes encode two subclasses of novel proline-rich glycoproteins with highly repetitive PX₁PX₂ motifs, RePRP1 and RePRP2. RePRP orthologs exist only in monocotyledonous plants, and their functions are virtually unknown. Rice RePRPs are heavily glycosylated with arabinose and glucose on multiple hydroxyproline residues. They are significantly different from arabinogalactan proteins that have glycan chains composed of arabinose and galactose. Transient and stable expressions of RePRP-green fluorescent protein reveal that a fraction of this protein is localized to the plasma membrane. In rice roots, ABA treatment increases RePRP expression preferentially in the elongation zone. Overexpression of RePRP in transgenic rice reduces root cell elongation in the absence of ABA, similar to the effect of ABA on wild-type roots. Conversely, simultaneous knockdown of the expression of RePRP1 and RePRP2 reduces the root sensitivity to ABA, indicating that RePRP proteins play an essential role in ABA/stress regulation of root growth and development. Moreover, rice RePRPs specifically interact with a polysaccharide, arabinogalactan, in a dosage-dependent manner. It is suggested that RePRP1 and RePRP2 are functionally redundant suppressors of root cell expansion and probably act through interactions with cell wall components near the plasma membrane.

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.

Progress toward the tomato fruit cell wall proteome

The plant cell wall (CW) compartment, or apoplast, is host to a highly dynamic proteome, comprising large numbers of both enzymatic and structural proteins. This reflects its importance as the interface between adjacent cells and the external environment, the presence of numerous extracellular metabolic and signaling pathways, and the complex nature of wall structural assembly and remodeling during cell growth and differentiation. Tomato fruit ontogeny, with its distinct phases of rapid growth and ripening, provides a valuable experimental model system for CW proteomic studies, in that it involves substantial wall assembly, remodeling, and coordinated disassembly. Moreover, diverse populations of secreted proteins must be deployed to resist microbial infection and protect against abiotic stresses. Tomato fruits also provide substantial amounts of biological material, which is a significant advantage for many types of biochemical analyses, and facilitates the detection of lower abundance proteins. In this review, we describe a variety of orthogonal techniques that have been applied to identify CW localized proteins from tomato fruit, including approaches that: target the proteome of the CW and the overlying cuticle; functional "secretome" screens; lectin affinity chromatography; and computational analyses to predict proteins that enter the secretory pathway. Each has its merits and limitations, but collectively they are providing important insights into CW proteome composition and dynamics, as well as some potentially controversial issues, such as the prevalence of non-canonical protein secretion.

Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals

Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance.

Plant cell wall proteomics: the leadership of Arabidopsis thaliana

Plant cell wall proteins (CWPs) progressively emerged as crucial components of cell walls although present in minor amounts. Cell wall polysaccharides such as pectins, hemicelluloses, and cellulose represent more than 90% of primary cell wall mass, whereas hemicelluloses, cellulose, and lignins are the main components of lignified secondary walls. All these polymers provide mechanical properties to cell walls, participate in cell shape and prevent water loss in aerial organs. However, cell walls need to be modified and customized during plant development and in response to environmental cues, thus contributing to plant adaptation. CWPs play essential roles in all these physiological processes and particularly in the dynamics of cell walls, which requires organization and rearrangements of polysaccharides as well as cell-to-cell communication. In the last 10 years, plant cell wall proteomics has greatly contributed to a wider knowledge of CWPs. This update will deal with (i) a survey of plant cell wall proteomics studies with a focus on Arabidopsis thaliana; (ii) the main protein families identified and the still missing peptides; (iii) the persistent issue of the non-canonical CWPs; (iv) the present challenges to overcome technological bottlenecks; and (v) the perspectives beyond cell wall proteomics to understand CWP functions.

Genome-wide analysis of the expansin gene superfamily reveals grapevine-specific structural and functional characteristics

BACKGROUND

Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP) comprises four distinct families: expansin A (EXPA), expansin B (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera) genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far.

METHODOLOGY/PRINCIPAL FINDINGS

We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon-intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa), compared to those from Arabidopsis thaliana and rice (Oryza sativa). We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering.

CONCLUSION

Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the functional characterization of grapevine gene families by combining phylogenetic analysis with global gene expression profiling.

Genetic variability of oxalate oxidase activity and elongation in water-stressed primary roots of diverse maize and rice lines

A previous study of maize primary roots under water stress showed pronounced increases in oxalate oxidase activity and apoplastic hydrogen peroxide in the apical region of the growth zone where cell elongation is maintained. We examined whether increased oxalate oxidase activity in water-stressed roots is conserved across diverse lines of maize and rice. The maize lines exhibited varied patterns of activity, with some lines lacking activity in the apical region. Moreover, none of the rice lines showed activity in the apical region. Also, although the genotypic response of root elongation to water stress was variable in both maize and rice, this was not correlated with the pattern of oxalate oxidase activity. Implications of these findings for root growth regulation under water stress are discussed.

Apoplastic hydrogen peroxide in the growth zone of the maize primary root under water stress. I. Increased levels are specific to the apical region of growth maintenance

Previous work on the adaptation of maize (Zea mays L.) primary root growth to water stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex. Cell wall proteomic analysis suggested that levels of apoplastic reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), may be modified in a region-specific manner within the growth zone of water-stressed roots. Apoplastic ROS may have wall loosening or tightening effects and may also have other growth regulatory functions. To gain an understanding of how apoplastic ROS levels change under water stress, cerium chloride staining was used in conjunction with transmission electron microscopy to examine the spatial distribution of apoplastic H2O2. The results revealed that apoplastic H2O2 levels increased specifically in the apical region of the growth zone under water stress, correlating spatially with the maintenance of cell elongation. The basal regions of the growth zone of water-stressed roots and the entire growth zone of well-watered roots exhibited relatively low levels of apoplastic H2O2. The increase in apoplastic H2O2 in the apical region under water stress probably resulted, at least in part, from a pronounced increase in oxalate oxidase activity in this region. By contrast, well-watered roots showed negligible oxalate oxidase activity throughout the growth zone. The results show that changes in apoplastic ROS levels in the root growth zone under water-deficit conditions are regulated in a spatially-specific manner, suggesting that this response may play an important role in maize root adaptation to water stress.

Proteomic analysis of tomato (Solanum lycopersicum) secretome

In fleshy fruits, fruit texture features are mainly related to chemical and mechanical properties of the cell wall. The description of tomato fruit cell wall proteome is a first step in the process of linking tomato genetic variability to fruit texture phenotypes. In this study, the proteome of 3 ripe tomato fruit lines with contrasted texture traits were studied. Weakly bound and soluble proteins were extracted from cell wall of the three cultivars using both destructive and non-destructive methods, respectively. Wall proteins were separated on 1D-PAGE, bands were excised and identified by LC-MS/MS. The software SignalP which searches for the leader peptide was used to discriminate between protein with or without signal peptide. In combine, seventy-five different cell wall proteins were recorded for both weakly bound and soluble cell wall fractions. The major identified functions included several proteins acting on polysaccharides, proteins involved in "lipid metabolism", proteins having interacting domain, "oxido-reductases" and "proteases" whose putative roles in ripe fruit cell wall is discussed. Several proteins with no obvious signal peptide, however, with accumulating supportive evidences to be bona fide wall proteins, were also identified. Some variations in protein repertories were observed among the lines, demonstrating the possibility to characterize cell wall protein genetic variability by such in muro proteome analyses.

Proteomic analysis of tomato (Solanum lycopersicum) secretome

In fleshy fruits, fruit texture features are mainly related to chemical and mechanical properties of the cell wall. The description of tomato fruit cell wall proteome is a first step in the process of linking tomato genetic variability to fruit texture phenotypes. In this study, the proteome of 3 ripe tomato fruit lines with contrasted texture traits were studied. Weakly bound and soluble proteins were extracted from cell wall of the three cultivars using both destructive and non-destructive methods, respectively. Wall proteins were separated on 1D-PAGE, bands were excised and identified by LC-MS/MS. The software SignalP which searches for the leader peptide was used to discriminate between protein with or without signal peptide. In combine, seventy-five different cell wall proteins were recorded for both weakly bound and soluble cell wall fractions. The major identified functions included several proteins acting on polysaccharides, proteins involved in "lipid metabolism", proteins having interacting domain, "oxido-reductases" and "proteases" whose putative roles in ripe fruit cell wall is discussed. Several proteins with no obvious signal peptide, however, with accumulating supportive evidences to be bona fide wall proteins, were also identified. Some variations in protein repertories were observed among the lines, demonstrating the possibility to characterize cell wall protein genetic variability by such in muro proteome analyses.

Cell wall proteomics of crops

Cell wall proteins play key roles in cell structure and metabolism, cell enlargement, signal transduction, responses to environmental stress, and many other physiological events. Agricultural crops are often used for investigating stress tolerance because cultivars with differing degrees of tolerance are available. Abiotic and biotic stress factors markedly influence the geographical distribution and yields of many crop species. Crop cell wall proteomics is of particular importance for improving crop productivity, particularly under unfavorable environmental conditions. To better understand the mechanisms underlying stress response in crops, cell wall proteomic analyses are being increasingly utilized. In this review, the methods of purification and purity assays of cell wall protein fractions from crops are described, and the results of protein identification using gel-based and gel-free proteomic techniques are presented. Furthermore, protein composition of the cell walls of rice, wheat, maize, and soybean are compared, and the role of cell wall proteins in crops under flooding and drought stress is discussed. This review will be useful for clarifying the role of the cell wall of crops in response to environmental stresses.

RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals

Dehydration inhibits petal expansion resulting in abnormal flower opening and results in quality loss during the marketing of cut flowers. We constructed a suppression subtractive hybridization library from rose (Rosa hybrida) flowers containing 3,513 unique expressed sequence tags and analyzed their expression profiles during cycles of dehydration. We found that 54 genes were up-regulated by the first dehydration, restored or even down-regulated by rehydration, and once again up-regulated by the second dehydration. Among them, we identified a putative NAC family transcription factor (RhNAC2). With transactivation activity of its carboxyl-terminal domain in yeast (Saccharomyces cerevisiae) cell and Arabidopsis (Arabidopsis thaliana) protoplast, RhNAC2 belongs to the NAC transcription factor clade related to plant development in Arabidopsis. A putative expansin gene named RhEXPA4 was also dramatically up-regulated by dehydration. Silencing RhNAC2 or RhEXPA4 in rose petals by virus-induced gene silencing significantly decreased the recovery of intact petals and petal discs during rehydration. Overexpression of RhNAC2 or RhEXPA4 in Arabidopsis conferred strong drought tolerance in the transgenic plants. RhEXPA4 expression was repressed in RhNAC2-silenced rose petals, and the amino-terminal binding domain of RhNAC2 bound to the RhEXPA4 promoter. Twenty cell wall-related genes, including seven expansin family members, were up-regulated in Arabidopsis plants overexpressing RhNAC2. These data indicate that RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals and that RhEXPA4 expression may be regulated by RhNAC2.

High-resolution imaging of Ca2+ , redox status, ROS and pH using GFP biosensors

Many plant response systems are linked to complex dynamics in signaling molecules such as Ca(2+) and reactive oxygen species (ROS) and to pH. Regulatory changes in these molecules can occur in the timeframe of seconds and are often limited to specific subcellular locales. Thus, to understand how Ca(2+) , ROS and pH form part of plants' regulatory networks, it is essential to capture their rapid dynamics with resolutions that span the whole plant to subcellular dimensions. Defining the spatio-temporal signaling 'signatures' of these regulators at high resolution has now been greatly facilitated by the generation of plants expressing a range of GFP-based bioprobes. For Ca(2+) and pH, probes such as the yellow cameleon Ca(2+) sensors (principally YC2.1 and 3.6) or the pHluorin and H148D pH sensors provide a robust suite of tools to image changes in these ions. For ROS, the tools are much more limited, with the GFP-based H(2) O(2) sensor Hyper representing a significant advance for the field. However, with this probe, its marked pH sensitivity provides a key challenge to interpretation without using appropriate controls to test for potentially coupled pH-dependent changes. Most of these Ca(2+) -, ROS- and pH-imaging biosensors are compatible with the standard configurations of confocal microscopes available to many researchers. These probes therefore represent a readily accessible toolkit to monitor cellular signaling. Their use does require appreciation of a minimal set of controls but these are largely related to ensuring that neither the probe itself nor the imaging conditions used perturb the biology of the plant under study.

Different peroxidase activities and expression of abiotic stress-related peroxidases in apical root segments of wheat genotypes with different drought stress tolerance under osmotic stress

One-week-old seedlings of Triticum aestivum L. cv. Plainsman V, a drought tolerant; and Cappelle Desprez, a drought sensitive wheat cultivar were subjected gradually to osmotic stress using polyethylene glycol (PEG 6000) reaching 400 mOsm on the 11th day. Compared to controls cv. Plainsman V maintained the root growth and relative water content of root tissues, while these parameters were decreased in the drought sensitive cv. Cappelle Desprez under PEG-mediated osmotic stress. Simultaneously, H(2)O(2) content in 1-cm-long apical segment of roots comprising the proliferation and elongation zone, showed a transient increase in cv. Plainsman V and a permanent raise in cv. Cappelle Desprez. Measurements of the transcript levels of selected class III peroxidase (TaPrx) coding sequences revealed significant differences between the two cultivars on the 9th day, two days after applying 100 mOsm PEG. The abundance of TaPrx04 transcript was enhanced transitionally in the root apex of cv. Plainsman V but decreased in cv. Cappelle Desprez under osmotic stress while the expression of TaPrx01, TaPrx03, TaPrx19, TaPrx68, TaPrx107 and TaPrx109-C decreased to different extents in both cultivars. After a transient decrease, activities of soluble peroxidase fractions of crude protein extracts rose in both cultivars on day 11, but the activities of cell wall-bound fractions increased only in cv. Cappelle Desprez under osmotic stress. Parallel with high H(2)O(2) content of the tissues, certain isoenzymes of covalently bound fraction in cv. Cappelle Desprez showed increased activity suggesting that they may limit the extension of root cell walls in this cultivar.

Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale

Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E. hyemale rhizomes using a GeLC-MS spectral-counting proteomics strategy. A total of 1,911 and 1,860 non-redundant proteins were identified in the rhizomes apical tip and elongation zone, respectively. Rhizome-characteristic proteins were determined by comparisons of the developing rhizome tissues to developing roots. A total of 87 proteins were found to be up-regulated in both horsetail rhizome tissues in relation to developing roots. Hierarchical clustering indicated a vast dynamic range in the regulation of the 87 characteristic proteins and revealed, based on the regulation profile, the existence of nine major protein groups. Gene ontology analyses suggested an over-representation of the terms involved in macromolecular and protein biosynthetic processes, gene expression, and nucleotide and protein binding functions. Spatial difference analysis between the rhizome apical tip and the elongation zone revealed that only eight proteins were up-regulated in the apical tip including RNA-binding proteins and an acyl carrier protein, as well as a KH domain protein and a T-complex subunit; while only seven proteins were up-regulated in the elongation zone including phosphomannomutase, galactomannan galactosyltransferase, endoglucanase 10 and 25, and mannose-1-phosphate guanyltransferase subunits alpha and beta. This is the first large-scale characterization of the proteome of a plant rhizome. Implications of the findings were discussed in relation to other underground organs and related species.

Physiological and molecular analysis of polyethylene glycol-induced reduction of aluminium accumulation in the root tips of common bean (Phaseolus vulgaris)

• Aluminium (Al) toxicity and drought are two major stress factors limiting common bean (Phaseolus vulgaris) production on tropical acid soils. Polyethylene glycol (PEG) treatment reduces Al uptake and Al toxicity. • The effect of PEG 6000-induced osmotic stress on the expression of genes was studied using SuperSAGE combined with next-generation sequencing and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for selected genes. • Less Al stress in PEG-treated roots was confirmed by decreased Al-induced up-regulation of MATE and ACCO genes. The withdrawal of PEG from the Al treatment solution restored the Al accumulation and reversed the expression of MATE and ACCO genes to the level of the treatment with Al alone. Using SuperSAGE, we identified 611 up- and 728 down-regulated genes in PEG-treated root tips, and the results were confirmed by qRT-PCR using 46 differentially expressed genes. Among the 12 genes studied in more detail, XTHa and BEG (down-regulated by PEG) and HRGP, bZIP, MYB and P5CS (up-regulated by PEG) recovered completely within 2 h after removal of PEG stress. • The results suggest that genes related to cell wall assembly and modification, such as XTHs, BEG and HRGP, play important roles in the PEG-induced decrease in cell wall porosity, leading to reduced Al accumulation in root tips.

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.

Large changes in anatomy and physiology between diploid Rangpur lime (Citrus limonia) and its autotetraploid are not associated with large changes in leaf gene expression

Very little is known about the molecular origin of the large phenotypic differentiation between genotypes arising from somatic chromosome set doubling and their diploid parents. In this study, the anatomy and physiology of diploid (2x) and autotetraploid (4x) Rangpur lime (Citrus limonia Osbeck) seedlings has been characterized. Growth of 2x was more vigorous than 4x although leaves, stems, and roots of 4x plants were thicker and contained larger cells than 2x that may have a large impact on cell-to-cell water exchanges. Leaf water content was higher in 4x than in 2x. Leaf transcriptome expression using a citrus microarray containing 21 081 genes revealed that the number of genes differentially expressed in both genotypes was less than 1% and the maximum rate of gene expression change within a 2-fold range. Six up-regulated genes in 4x were targeted to validate microarray results by real-time reverse transcription-PCR. Five of these genes were apparently involved in the response to water deficit, suggesting that, in control conditions, the genome expression of citrus autotetraploids may act in a similar way to diploids under water-deficit stress condition. The sixth up-regulated gene which codes for a histone may also play an important role in regulating the transcription of growth processes. These results show that the large phenotypic differentiation in 4x Rangpur lime compared with 2x is not associated with large changes in genome expression. This suggests that, in 4x Rangpur lime, subtle changes in gene expression may be at the origin of the phenotypic differentiation of 4x citrus when compared with 2x.

Comparative proteomics analysis of the root apoplasts of rice seedlings in response to hydrogen peroxide

Background

Plant apoplast is the prime site for signal perception and defense response, and of great importance in responding to environmental stresses. Hydrogen peroxide (H₂O₂) plays a pivotal role in determining the responsiveness of cells to stress. However, how the apoplast proteome changes under oxidative condition is largely unknown. In this study, we initiated a comparative proteomic analysis to explore H₂O₂-responsive proteins in the apoplast of rice seedling roots.

Methodology/Principal Findings

14-day-old rice seedlings were treated with low concentrations (300 and 600 µM) of H₂O₂ for 6 h and the levels of relative electrolyte leakage, malondialdehyde and H₂O₂ were assayed in roots. The modified vacuum infiltration method was used to extract apoplast proteins of rice seedling roots, and then two-dimensional electrophoresis gel analysis revealed 58 differentially expressed protein spots under low H₂O₂ conditions. Of these, 54 were successfully identified by PMF or MS/MS as matches to 35 different proteins including known and novel H₂O₂-responsive proteins. Almost all of these identities (98%) were indeed apoplast proteins confirmed either by previous experiments or through publicly available prediction programs. These proteins identified are involved in a variety of processes, including redox homeostasis, cell wall modification, signal transduction, cell defense and carbohydrate metabolism, indicating a complex regulative network in the apoplast of seedling roots under H₂O₂ stress.

Conclusions/Significance

The present study is the first apoplast proteome investigation of plant seedlings in response to H₂O₂ and may be of paramount importance for the understanding of the plant network to environmental stresses. Based on the abundant changes in these proteins, together with their putative functions, we proposed a possible protein network that provides new insights into oxidative stress response in the rice root apoplast and clues for the further functional research of target proteins associated with H₂O₂ response.

In vivo imaging of Ca2+, pH, and reactive oxygen species using fluorescent probes in plants

Changes in the levels of Ca(2+), pH, and reactive oxygen species (ROS) are recognized as key cellular regulators involved in diverse physiological and developmental processes in plants. Critical to understanding how they exert such widespread control is an appreciation of their spatial and temporal dynamics at levels from organ to organelle and from seconds to many hours. With appropriate controls, fluorescent sensors can provide a robust approach with which to quantify such changes in Ca(2+), pH, and ROS in real time, in vivo. The fluorescent cellular probes available for visualization split into two broad classes: (a) dyes and (b) an increasingly diverse set of genetically encoded sensors based around green fluorescent proteins (GFPs). The GFP probes in particular can be targeted to well-defined subcellular locales, offering the possibility of high-resolution mapping of these signals within the cell.

Interaction between environmental factors affects the accumulation of root proteins in hydroponically grown Eucalyptus globulus (Labill.)

Eucalyptus globulus (Labill.) is used for pulp and paper production worldwide. In this report we studied changes in protein expression in one osmotically stressed elite clone widely used in industrial plantations in Spain. High molecular weight polyethylene glycol (PEG) was used as an osmoticum in the growing medium. Roots of rooted cuttings were sampled after 3 and 36 h of treatment. Water potential and abscissic acid content were measured in shoot and root apices to characterize the physiological states of the plants. Total soluble proteins from roots were extracted and separated using two-dimensional gel electrophoresis (2-DE). Gels were stained with Coomassie brillant blue for quantitative analysis of protein accumulation. From a total of 406 reproducible spots, 34 were found to be differentially expressed depending on treatment (osmotic versus control condition) and/or stress duration (3 h versus 36 h), and were further characterized by tandem mass spectrometry. Several proteins were reliably identified including adenosine kinase, actin, stress-related proteins as well as proteins associated to cellular processes, among which some residents of the endoplasmic reticulum. This study constitutes the first investigation of the root proteome in this important forest tree genus.

Identification of extracellular matrix proteins of rice (Oryza sativa L.) involved in dehydration-responsive network: a proteomic approach

Water-deficit or dehydration impairs almost all physiological processes and greatly influences the geographical distribution of many crop species. It has been postulated that higher plants rely mostly on induction mechanisms to maintain cellular integrity during stress conditions. Plant cell wall or extracellular matrix (ECM) forms an important conduit for signal transduction between the apoplast and symplast and acts as front-line defense, thereby playing a key role in cell fate decision under various stress conditions. To better understand the molecular mechanism of dehydration response in plants, four-week-old rice seedlings were subjected to progressive dehydration by withdrawing water and the changes in the ECM proteome were examined using two-dimensional gel electrophoresis. Dehydration-responsive temporal changes revealed 192 proteins that change their intensities by more than 2.5-fold, at one or more time points during dehydration. The proteomic analysis led to the identification of about 100 differentially regulated proteins presumably involved in a variety of functions, including carbohydrate metabolism, cell defense and rescue, cell wall modification, cell signaling and molecular chaperones, among others. The differential rice proteome was compared with the dehydration-responsive proteome data of chickpea and maize. The results revealed an evolutionary divergence in the dehydration response as well as organ specificity, with few conserved proteins. The differential expression of the candidate proteins, in conjunction with previously reported results, may provide new insight into the underlying mechanisms of the dehydration response in plants. This may also facilitate the targeted alteration of metabolic routes in the cell wall for agricultural and industrial exploitation.