Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins

Analysis of Physiological Indicators Associated with Drought Tolerance in Wheat under Drought and Re-Watering Conditions

Wheat (Triticum aestivum L.) production is severely threatened by an increase in the frequency of drought events. It is crucial to determine stable and effective morphological, physiological, and associated oxidative stress indicators, to evaluate the drought tolerance of wheat for breeding and cultivation. Therefore, the cultivars Luohan 22 (LH 22, drought-tolerant) and Zhengmai 366 (ZM 366, drought-sensitive) were used as experimental materials to analyze the changes in 12 physiological and biochemical indicators, as well as the yield, when the stress was prolonged to different times. Re-watering after 6 days of drought can effectively alleviate the associated oxidative stress of drought to wheat. The physiological responses of plants were reversible when they were re-watered in the range of 6 to 12 days after drought. The degree of recovery of LH 22 was higher than that of ZM 366. Afterwards, seven indicators, including stomatal conductance, proline, malondialdehyde, soluble sugar, hexokinase, glucose, and the non-photochemical quenching parameter, were screened out to characterize tolerance of wheat to drought using the multivariate statistical analytical method. This study further investigated the method of evaluating and indexing tolerance of wheat to drought, from the physiological and biochemical levels. This study can provide a theoretical basis and reference for the selection of wheat cultivars to breed and cultivate against drought stress.

Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants.

Modulation of photosynthesis and other proteins during water-stress

Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.

Mass spectrometry-based forest tree metabolomics

Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.

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.

First record of off-season flowering in Populus deltoides from India: paradigm of climate change indicator

Populus deltoides is a fast-growing woody species possessing plethora of industrial applications. This species evolutionarily developed unisexual male and female catkin inflorescence on separate trees. Flowering usually occurs during early spring before the development of foliage, where buds appear near axils or at the extending shoots. In 2019, surveys were undertaken to study the flowering pattern of P. deltoides in the states of Punjab, Haryana, Uttar Pradesh and Uttarakhand in northern India. Interestingly, an anomalous flowering behaviour (appearance of off-season male catkins during autumn, i.e. October) was observed in a plantation trial at Kapurthala, Punjab. The male catkins were 2.7-3.1 ± 0.07 cm long and 0.3-0.5 ± 0.03 cm wide, which is significant for flowering and liberation of pollen grains. Preliminary results suggested that climatic factors, such as episodes of high or low temperature and the precipitation variation forcing the tree species to behave differently. Unearthing the climate-driven off-season flowering in other tree species alluded the stimulation of phytohormones, such as gibberellic and salicylic acid concentrations influencing the flowering time, therefore, needs further investigation in case of P. deltoides. Overall, this work provides early clues of changing climatic scenario altering the flowering pattern of a tropical forestry tree species.

Metabolic profiles of moso bamboo in response to drought stress in a field investigation

An increasing number of moso bamboo habitats are suffering severe drought events. The improvement in our understanding of the mechanisms of drought-resistance in moso bamboo benefits their genetic improvement and maintenance of forest sustainability. Here, we investigated the metabolic changes across the annual growth cycle of moso bamboo in the field under drought stress using liquid chromatography coupled to mass spectrometry (LC-MS) based on untargeted metabolomic profiling. Our results showed that the metabolic profiles induced by drought stress were relatively consistent among the three growth stages. Specifically, most responsive metabolites exhibited enhanced accumulation under drought stress, including anthocyanins, glycosides, organic acids, amino acids, and sugars and sugar alcohols. The potential metabolism pathways involved in the response to drought stress were mainly included into amino acid metabolism and sugar metabolism pathways. Five common responsive metabolic pathways were found among three growth stages, including linoleic acid metabolism, ubiquinone and other terpenoid-quinone biosynthesis, tyrosine metabolism, starch and sucrose metabolism and isoquinoline alkaloid biosynthesis. Overall, our findings provide new insights into the responsive mechanisms of the moso bamboo under drought stress in terms of metabolic profiles.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows adaptation of grass pollen composition

MALDI time-of-flight mass spectrometry (MALDI-TOF MS) has become a widely used tool for the classification of biological samples. The complex chemical composition of pollen grains leads to highly specific, fingerprint-like mass spectra, with respect to the pollen species. Beyond the species-specific composition, the variances in pollen chemistry can be hierarchically structured, including the level of different populations, of environmental conditions or different genotypes. We demonstrate here the sensitivity of MALDI-TOF MS regarding the adaption of the chemical composition of three Poaceae (grass) pollen for different populations of parent plants by analyzing the mass spectra with partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA). Thereby, variances in species, population and specific growth conditions of the plants were observed simultaneously. In particular, the chemical pattern revealed by the MALDI spectra enabled discrimination of the different populations of one species. Specifically, the role of environmental changes and their effect on the pollen chemistry of three different grass species is discussed. Analysis of the group formation within the respective populations showed a varying influence of plant genotype on the classification, depending on the species, and permits conclusions regarding the respective rigidity or plasticity towards environmental changes.

Drought-tolerant and drought-sensitive genotypes of maize (Zea mays L.) differ in contents of endogenous brassinosteroids and their drought-induced changes

The contents of endogenous brassinosteroids (BRs) together with various aspects of plant morphology, water management, photosynthesis and protection against cell damage were assessed in two maize genotypes that differed in their drought sensitivity. The presence of 28-norbrassinolide in rather high quantities (1-2 pg mg-1 fresh mass) in the leaves of monocot plants is reported for the first time. The intraspecific variability in the presence/content of the individual BRs in drought-stressed plants is also described for the first time. The drought-resistant genotype was characterised by a significantly higher content of total endogenous BRs (particularly typhasterol and 28-norbrassinolide) compared with the drought-sensitive genotype. On the other hand, the drought-sensitive genotype showed higher levels of 28-norcastasterone. Both genotypes also differed in the drought-induced reduction/elevation of the levels of 28-norbrassinolide, 28-norcastasterone, 28-homocastasterone and 28-homodolichosterone. The differences observed between both genotypes in the endogenous BR content are probably correlated with their different degrees of drought sensitivity, which was demonstrated at various levels of plant morphology, physiology and biochemistry.

Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways

The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem. Using microarray chips, differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were identified for each water regime. The rewatering condition was associated with the highest variations of both gene expression and DNA methylation. Changes in methylation were observed particularly in the body of expressed genes and to a lesser extent in transposable elements. Together, DEGs and DMRs were significantly enriched in genes related to phytohormone metabolism or signaling pathways. Altogether, shoot apical meristem responses to changes in water availability involved coordinated variations in DNA methylation, as well as in gene expression, with a specific targeting of genes involved in hormone pathways, a factor that may enable phenotypic plasticity.

Variability studies of allochthonous stone pine (Pinus pinea L.) plantations in Chile through nut protein profiling

Stone pine (Pinus pinea) is characterized by low differentiation of growth parameters, high phenotypic plasticity and low genetic variability; detecting its diversity in introduced Chilean populations is therefore relevant for conservation and breeding programs. Here, variability among allochthonous Stone pine populations in Chile was explored using electrophoresis-based proteomic analysis of pine nuts. Cones from 30 populations distributed along a climatic gradient in Chile were surveyed and sampled, and proteins were extracted from seed flour using the TCA-acetone precipitation protocol. Extracts were subjected to SDS-PAGE and 2-DE for protein resolution, gel images captured, and spot or bands intensity quantified and subjected to statistical analysis (ANOVA, unsupervised Hierarchical Analysis Clustering and PLS regression). Protein yield ranged among populations from 161.7 (North populations) to 298.7 (South populations) mg/g dry weight. A total of 50 bands were resolved by SDS-PAGE in the 6.5-200 kDa Mr. range, of which 17 showed quantitative or qualitative differences, with 12 proteins identified. Pine nut extracts from the most distant populations were analyzed by 2-DE and a total of 129 differential spots were observed, out of which 13 were proposed as putative protein markers of variability. Out of the 129 spots, 118 proteins were identified after MALDI-TOF/TOF analysis. Identified proteins were classified into two principal categories: reserve and stress related. We provide the first protein map of P. pinea nuts. The use of a proteomic approach was useful to detect variability of Stone pine across three Chilean macrozones, with correlations between protein profiles and geoclimatic parameters, suggesting a new approach to study the variability of this species.

BIOLOGICAL SIGNIFICANCE

This study presents the first protein map of Stone pine nuts, relevant for the advancement of protein characterization in pine nuts. Putative protein markers are proposed, evidencing that a proteomic approach may be useful to detect variability of Stone pine across Chilean macrozones, suggesting a new approach to study the variability of this species, which may also be extrapolated to other forest fruit species.

Unraveling physiological, biochemical and molecular mechanisms involved in olive (Olea europaea L. cv. Chétoui) tolerance to drought and salt stresses

Olive (Olea europaea L.) is an economically important crop for the Mediterranean basin, where prolonged drought and soil salinization may occur. This plant has developed a series of mechanisms to tolerate and grow under these adverse conditions. By using an integrated approach, we described in Chétoui olive cultivar the changes in plant growth, oxidative damage and osmolyte accumulation in leaves, in combination with corresponding changes in physiological parameters and proteome. Our results showed, under both stress conditions, a greater growth reduction of the aboveground plant organs than of the underground counterparts. This was associated with a reduction of all photosynthetic parameters, the integrity of photosystem II and leaf nitrogen content, and corresponding representation of photosynthetic apparatus proteins, Calvin-Benson cycle and nitrogen metabolism. The most significant changes were observed under the salinity stress condition. Oxidative stress was also observed, in particular, lipid peroxidation, which could be tentatively balanced by a concomitant photoprotective/antioxidative increase of carotenoid levels. At the same time, various compensative mechanisms to cope with nitrogen source demands and to control plant cell osmolarity were also shown by olive plants under these stresses. Taken together, these findings suggest that the Chétoui variety is moderately sensitive to both drought and salt stress, although it has greater ability to tolerate water depletion.

Gene regulation network behind drought escape, avoidance and tolerance strategies in black poplar (Populus nigra L.)

Drought is the major environmental problem limiting the productivity and survival of plant species. Here, previously identified three black poplar genotypes having contrasting response to drought were subjected to gradual soil water depletion in a pot trial to identify their physiological, morphological and antioxidation related adaptations. We also performed a microarray based transcriptome analyses on the leaves of genotypes by using Affymetrix poplar Genome Array containing 56,000 transcripts. Phenotypic analyses of each genotype confirmed their differential adaptations to drought that could be classified as drought escape, avoidance and tolerance. Comparative transcriptomic analysis indicated highly divergent gene expression patterns among the genotypes in response to drought and post drought re-watering (PDR). We identified 10641, 3824 and 9411 transcripts exclusively regulated in drought escape, avoidance and tolerant genotypes, respectively. The key genes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein folding, redox homeostasis, secondary metabolic process and cell wall component biogenesis, were affected by drought stresses in the leaves of these genotypes. Transcript isoforms showed increased expression specificity in the genes coding for bark storage proteins and small heat shock proteins in drought tolerant genotype. On the other hand, drought-avoiding genotype specifically induced the transcripts annotated to the genes functional in secondary metabolite production that linked to enhanced leaf water content and growth performance under drought stress. Transcriptome profiling of drought escape genotype indicated specific regulation of the genes functional in programmed cell death and leaf senescence. Specific upregulation of GTP cyclohydrolase II and transcription factors (WRKY and ERFs) in only this genotype were associated to ROS dependent signalling pathways and gene regulation network responsible in induction of many degrading enzymes acting on cell wall carbohydrates, fatty acids and proteins under drought stress. Our findings provide new insights into the transcriptome dynamics and components of regulatory network associated with drought adaptation strategies.

Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

Drought-induced changes in photosynthetic apparatus and antioxidant components of wheat (Triticum durum Desf.) varieties

Water deficit is a key factor influencing the yield and quality of crops. In the present study, the photosynthetic responses by means of chlorophyll fluorescence of chloroplasts, thylakoid membrane proteins, and antioxidant components were analyzed in wheat (Triticum durum Desf.) plants differing in their tolerance to drought. Two durum winter wheat varieties, Barakatli 95 (drought tolerant) and Garagylchyg 2 (drought sensitive) were grown under field well-watered and drought conditions. It was found that contents of the PS I core (CPI) with Mr of 123 kD and apoprotein P700 with Mr of 63 kD were relatively higher in Barakatli 95 variety under drought stress compared with the control plants. Synthesis of α- and β-subunits of CF₁ ATP-synthase complex with Mr of 55 and 53.5 kD also slightly increased in the tolerant Barakatli 95 and decreased in the drought sensitive variety Garagylchyg 2. A decrease in the intensity of 30 kD band and a significant increase were found in the content of the 25-16 kD region in Garagylchyg 2 variety. The synthesis of 60 kD and content of low molecular mass polypeptides (21.5 and 12 kD) were increased in the tolerant genotype Barakatli 95. The intensity of peaks at 687, 695, and 742 nm considerably increases in the fluorescence spectra (77 K) of chloroplasts isolated from the sensitive variety Garagylchyg 2, and there is a stimulation of the ratio of fluorescence band intensity F687/F740. At the same time, higher level of glycine betaine was found in the drought tolerant variety compared with the control one throughout the different periods of growth.

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy.

Characterization of the orthodox Pinus occidentalis seed and pollen proteomes by using complementary gel-based and gel-free approaches

This work presents an analysis of Pinus occidentalis pollen and seed proteomes, in which both gel-based and gel-free approaches have been used. Proteins were extracted from P. occidentalis seeds and pollen by using the TCA/acetone/phenol precipitation protocol, and protein extracts were subjected to 1- and 2-DE coupled to MALDI-TOF-TOF as well as to shotgun (nLC-LTQ-Orbitrap) analysis. All bands (1-DE) and the most abundant spots (2-DE) were excised, trypsin digested and the resulting peptides analyzed by MALDI TOF/TOF. In order to increase the proteome coverage, a gel free approach was used. Proteins were identified from mass spectra by using three different databases, including UniProtKB, NCBI and a Pinus spp. custom database [2]. The gel-based approach resulted in 42 (seeds) and 94 (pollen) protein identifications, while the shotgun approach permitted the identification of 187 (seed) and 960 (pollen) proteins. Proteins were classified based on their corresponding functional categories. In seeds, storage proteins were the most abundant ones, and some allergens and proteases were also identified. In pollen proteins related to general metabolism were the most predominant. Data are compared and discussed from a methodological and biological point of view, taking into account the particularities of the seed and pollen organs.

BIOLOGICAL SIGNIFICANCE

In this work we characterized P. occidentalis proteome with seeds and pollen samples implementing two complementary approaches for the analysis. We found a high content of storage protein, stress response and metabolism related proteins in the seed proteome. Similarly, in the pollen proteome we found predominant groups of proteins related to metabolism and stress response.

Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean

Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.

Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis

Eucalyptus species are the most widely hardwood planted in the world. It is one of the successful examples of commercial forestry plantation in Brazil and other tropical and subtropical countries. The tree is valued for its rapid growth, adaptability and wood quality. Wood formation is the result of cumulative annual activity of the vascular cambium. This cambial activity is generally related to the alternation of cold and warm, and/or dry and rainy seasons. Efforts have focused on analysis of cambial zone in response to seasonal variations in trees from temperate zones. However, little is known about the molecular changes triggered by seasonal variations in trees from tropical countries. In this work we attempted to establish a global view of seasonal alterations in the cambial zone of Eucalyptus grandis Hill ex Maiden, emphasizing changes occurring in the carbon metabolism. Using transcripts, proteomics and metabolomics we analyzed the tissues harvested in summer-wet and winter-dry seasons. Based on proteomics analysis, 70 proteins that changed in abundance were successfully identified. Transcripts for some of these proteins were analyzed and similar expression patterns were observed. We identified 19 metabolites differentially abundant. Our results suggest a differential reconfiguration of carbon partioning in E. grandis cambial zone. During summer, pyruvate is primarily metabolized via ethanolic fermentation, possibly to regenerate NAD(+) for glycolytic ATP production and cellular maintenance. However, in winter there seems to be a metabolic change and we found that some sugars were highly abundant. Our results revealed a dynamic change in E. grandis cambial zone due to seasonality and highlight the importance of glycolysis and ethanolic fermentation for energy generation and maintenance in Eucalyptus, a fast growing tree.

First proteome study of sporadic flowering in bamboo species (Bambusa vulgaris and Dendrocalamus manipureanus) reveal the boom is associated with stress and mobile genetic elements

Bamboo species are the fastest-growing plants having a long vegetative cycle. Abrupt switching from the vegetative phase to the reproductive phase via sporadic flowering boom, occasionally leads to death of bamboo clumps, and threatens the existence of many bamboo species. To apprehend the molecular mechanism driving sporadic flowering, proteome changes in the initial and advanced floral buds of two edible bamboo species (Bambusa vulgaris and Dendrocalamus manipureanus) was dissected by two-dimensional gel electrophoresis (2-DE). A total of 39 differentially expressed peptide spots were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). In both B. vulgaris and D. manipureanus, identified proteins were categorized as transposon-related, defence and stress-related, cell cycle related, metabolism related, signal transduction related, and some lacked known putative domains. Proteins such as SEPALLATA3, ubiquitin, histone 3, thaumatin-like protein, putative tethering factor, SF-assemblin, polyubiquitin, mitochondrial carrier-like protein and RPT2-like protein were significantly expressed. Differences in D. manipureanus and B. vulgaris suggested that bamboo species have diverse 'drivers' or 'passengers' genes that govern natural sporadic flowering boom. This first floral proteomics analysis of bamboos revealed that sporadic boom is a highly energetic process, associated with stress elements, mobile genetic elements and signal transduction cross-talk elements.

Physiological and proteome analysis suggest critical roles for the photosynthetic system for high water-use efficiency under drought stress in Malus

Water use efficiency is an important indicator for plant adaptation and resistance to drought conditions. We previously found that under moderate drought stress, the water use efficiency of cv. 'Qinguan' apple (Malus domestica Borkh.) (tolerant to drought) was enhanced, while that of cv. 'Naganofuji No. 2' was not enhanced. In this research, we also found that instantaneous water-use efficiency of cv. 'Qinguan' was higher than that of cv. 'Naganofuji No. 2', mainly because of its higher net photosynthesis rate. To dissect the potential mechanisms underlying this phenomenon, we performed a comparative iTRAQ-based proteomics analysis with leaves of drought-treated cv. 'Qinguan' and 'Naganofuji No. 2'. We identified 4078 proteins, of which 594 were differentially abundant between drought and well-watered leaves. The majority of increased proteins were predicted to be involved in photosynthetic pathway in drought treated cv. 'Qinguan' leaves, indicating that regulation of photosynthesis plays an important role for higher water use efficiency under drought stress. Enzyme activity assays were performed to validate the proteomics data. Our results suggested that the main regulatory mechanisms for high water use efficiency of cv. 'Qinguan' under moderate drought stress included the maintaining of Calvin cycle function by increasing key enzymes, stabilization of photosynthetic electron transfer and keeping reactive oxygen species at normal level by regulation of photosynthetic electron transfer chain, photorespiration and reactive oxygen species scavenging capability, thus prevented photoinhibition, reduced reactive oxygen species production and enhanced net photosynthesis rate. In addition, the response of signal regulatory proteins and abiotic stress-responsive proteins to drought also helped plants to cope with such stress.

Identification of Leaf Proteins Differentially Accumulated between Wheat Cultivars Distinct in Their Levels of Drought Tolerance

The drought-tolerant ‘Ningchun 47’ (NC47) and drought-sensitive ‘Chinese Spring’ (CS) wheat (Triticum aestivum L.) cultivars were treated with different PEG6000 concentrations at the three-leaf stage. An analysis on the physiological and proteomic changes of wheat seedling in response to drought stress was performed. In total, 146 differentially accumulated protein (DAP) spots were separated and recognised using two-dimensional gel electrophoresis. In total, 101 DAP spots representing 77 unique proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. These proteins were allocated to 10 groups according to putative functions, which were mainly involved in carbon metabolism (23.4%), photosynthesis/respiration (22.1%) and stress/defence/detoxification (18.2%). Some drought stress-related proteins in NC47, such as enolase, 6-phosphogluconate dehydrogenase, Oxygen-evolving enhancer protein 2, fibrillin-like protein, 2-Cys peroxiredoxin BAS1 and 70-kDa heat shock protein, were more upregulated than those in CS. Multivariate principal components analysis revealed obvious differences between the control and treatments in both NC47 and CS, while cluster analysis showed that the DAPs displayed five and six accumulation patterns in NC47 and CS, respectively. Protein–protein interaction network analysis showed that some key DAPs, such as 2-Cys peroxiredoxin BAS1, RuBisCO large subunit-binding protein, 50S ribosomal protein L1, 6-phosphogluconate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase isoenzyme and 70-kDa heat shock protein, with upregulated accumulation in NC47, had complex interactions with other proteins related to amino acid metabolism, carbon metabolism, energy pathway, signal transduction, stress/defence/detoxification, protein folding and nucleotide metabolism. These proteins could play important roles in drought-stress tolerance and contribute to the relatively stronger drought tolerance of NC47.

PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data

miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear, especially when microarray data is used. Fortunately, due to the low sequencing cost, small RNA and RNA sequencing are routinely processed and we may be able to infer regulation relationships between miRNAs and mRNAs more accurately by using sequencing data. However, no method is developed specifically for sequencing data. Thus we developed PlantMirnaT, a new miRNA-mRNA integrated analysis system. To fully leverage the power of sequencing data, three major features are developed and implemented in PlantMirnaT. First, we implemented a plant-specific short read mapping tool based on recent discoveries on miRNA target relationship in plant. Second, we designed and implemented an algorithm considering miRNA targets in the full intragenic region, not just 3' UTR. Lastly but most importantly, our algorithm is designed to consider quantity of miRNA expression and its distribution on target mRNAs. The new algorithm was used to characterize rice under drought condition using our proprietary data. Our algorithm successfully discovered that two miRNAs, miRNA1425-5p, miRNA 398b, that are involved in suppression of glucose pathway in a naturally drought resistant rice, Vandana. The system can be downloaded at https://sites.google.com/site/biohealthinformaticslab/resources.

Redox proteomics and physiological responses in Cistus albidus shrubs subjected to long-term summer drought followed by recovery

The interaction between enzymatic and non-enzymatic antioxidants, endogenous levels of ABA and ABA-GE, the rapid recuperation of photosynthetic proteins under re-watering as well the high level of antioxidant proteins in previously drought-stressed plants under re-watering conditions, will contribute to drought resistance in plants subjected to a long-term drought stress under Mediterranean field conditions. This work provides an overview of the mechanisms of Cistus albidus acclimation to long-term summer drought followed by re-watering in Mediterranean field conditions. To better understand the molecular mechanisms of drought resistance in these plants, a proteomic study using 2-DE and MALDI-TOF/TOF MS/MS was performed on leaves from these shrubs. The analysis identified 57 differentially expressed proteins in water-stressed plants when contrasted to well watered. Water-stressed plants showed an increase, both qualitatively and quantitatively, in HSPs, and downregulation of photosynthesis and carbon metabolism enzymes. Under drought conditions, there was considerable upregulation of enzymes related to redox homeostasis, DHA reductase, Glyoxalase, SOD and isoflavone reductase. However, upregulation of catalase was not observed until after re-watering was carried out. Drought treatment caused an enhancement in antioxidant defense responses that can be modulated by ABA, and its catabolites, ABA-GE, as well as JA. Furthermore, quantification of protein carbonylation was shown to be a useful marker of the relationship between water and oxidative stress, and showed that there was only moderate oxidative stress in C. albidus plants subjected to water stress. After re-watering plants recovered although the levels of ABA-GE and antioxidant enzymes still remain higher than in well-watered plants. We expect that our results will provide new data on summer acclimation to drought stress in Mediterranean shrubs.

Protein expression changes during cotton fiber elongation in response to drought stress and recovery

An investigation to better understand the molecular mechanism of cotton (Gossypium hirsutum L.) fiber elongation in response to drought stress and recovery was conducted using a comparative proteomics analysis. Cotton plants (cv. NuCOTN 33B) were subjected to water deprivation for 10 days followed by a recovery period (with watering) of 5 days. The temporal changes in total proteins in cotton fibers were examined using 2DE. The results revealed that 163 proteins are significantly drought responsive. MS analysis led to the identification of 132 differentially expressed proteins that include some known as well as some novel drought-responsive proteins. These drought responsive fiber proteins in NuCOTN 33B are associated with a variety of cellular functions, i.e. signal transduction, protein processing, redox homeostasis, cell wall modification, metabolisms of carbon, energy, lipid, lignin, and flavonoid. The results suggest that the enhancement of the perception of drought stress, a new balance of the metabolism of the biosynthesis of cell wall components and cytoskeleton homeostasis plays an important role in the response of cotton fibers to drought stress. Overall, the current study provides an overview of the molecular mechanism of drought response in cotton fiber cells.

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.

2-DE proteomics analysis of drought treated seedlings of Quercus ilex supports a root active strategy for metabolic adaptation in response to water shortage

Holm oak is a dominant tree in the western Mediterranean region. Despite being well adapted to dry hot climate, drought is the main cause of mortality post-transplanting in reforestation programs. An active response to drought is critical for tree establishment and survival. Applying a gel-based proteomic approach, dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Stress was monitored by changes in water status, plant growth, and electrolyte leakage. Contrary to leaves, holm oak roots responded readily to water shortage at physiological level by growth inhibition, changes in water status and membrane stability. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and separated by two-dimensional electrophoresis. Coomassie colloidal stained gel images were analyzed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Data are available via ProteomeXchange with identifier PXD002484. Identified proteins were classified into functional groups: metabolism, protein biosynthesis and proteolysis, defense against biotic stress, cellular protection against abiotic stress, intracellular transport. Several enzymes of the carbohydrate metabolism decreased in abundance in roots under drought stress while some related to ATP synthesis and secondary metabolism increased. Results point at active metabolic adjustment and mobilization of the defense system in roots to actively counteract drought stress.

Improved tolerance to drought stress after anthesis due to priming before anthesis in wheat (Triticum aestivum L.) var. Vinjett

Drought stress occurring during the reproductive growth stage leads to considerable reductions in crop production and has become an important limiting factor for food security globally. In order to explore the possible role of drought priming (pre-exposure of the plants to mild drought stress) on the alleviation of a severe drought stress event later in development, wheat plants were subjected to single or double mild drought episodes (soil relative water content around 35-40%) before anthesis and/or to a severe drought stress event (soil relative water content around 20-25%) 15 d after anthesis. Here, single or double drought priming before anthesis resulted in higher grain yield than in non-primed plants under drought stress during grain filling. The photosynthesis rate and ascorbate peroxidase activity were higher while malondialdehyde content was lower in primed plants than in the non-primed plants under drought stress during grain filling. Proteins in flag leaves differently expressed by the priming and drought stress were mainly related to photosynthesis, stress defence, metabolism, molecular chaperone, and cell structure. Furthermore, the protein abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit, Rubisco activase and ascorbate peroxidase were upregulated in primed plants compared with non-primed plants under drought stress during grain filling. In conclusion, the altered protein expression and upregulated activities of photosynthesis and ascorbate peroxidase in primed plants may indicate their potential roles in alleviating a later-occurring drought stress episode, thereby contributing to higher wheat grain yield under drought stress during grain filling.

Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement

Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed.

Glycolytic enzyme activities and gene expression in Cicer arietinum exposed to water-deficit stress

The specific activities and transcript levels of glycolytic enzymes were examined in shoots of chickpea (Cicer arietinum L.) cultivars, Pusa362 (drought tolerant) and SBD377 (drought sensitive), subjected to water-deficit stress 30 days after sowing. Water-deficit stress resulted in decrease in relative water content, chlorophyll content, plant dry weight, and NADP/NADPH ratio and increase in NAD/NADH ratio in both the cultivars. A successive decline in the specific activities of fructose-1,6-bisphosphate aldolase (aldolase), 3-phosphoglycerate kinase (PGK), and NADP-glyceraldehyde-3-phosphate dehydrogenase (NADP-GAPDH) and elevation in the specific activities of phosphoglycerate mutase (PGM) and triosephosphate isomerase (TPI) was observed in both the cultivars under stress as compared to their respective control plants. The specific activities of hexokinase, fructose-6-phosphate kinase (PFK), and NAD-GAPDH were least affected. The transcript levels of PGK and NADP-GAPDH decreased and that of glucose-6-phosphate isomerase (GPI), PGM, and PFK increased in response to water-deficit stress while water-deficit stress had no effect on the steady-state transcript levels of hexokinase, aldolase, TPI, and NAD-GAPDH. The results suggest that under water-deficit stress, the activities and transcript levels of most of the glycolytic enzymes are not significantly affected, except the increased activity and transcript level of PGM and decreased activities and transcript levels of PGK and NADP-GAPDH. Further, the glycolytic enzymes do not show much variation between the tolerant and sensitive cultivars under water deficit.

Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif

BACKGROUND

Plant and animal pathogenic fungus Cochliobolus lunatus cause great economic damages worldwide every year. C. lunatus displays an increased temperature dependent-virulence to a wide range of hosts. Nonetheless, this phenomenon is poorly understood due to lack of insights on the coordinated secretome weaponries produced by C. lunatus under heat-stress conditions on putative hosts. To understand the mechanism better, we dissected the secretome of C. lunatus interacting with potato (Solanum tuberosum L.) leaf at different temperature regimes.

RESULTS

C. lunatus produced melanized colonizing hyphae in and on potato leaf, finely modulated the ambient pH as a function of temperature and secreted diverse set of proteins. Using two dimensional gel electrophoresis (2-D) and mass spectrometry (MS) technology, we observed discrete secretomes at 20°C, 28°C and 38°C. A total of 21 differentially expressed peptide spots and 10 unique peptide spots (that did not align on the gels) matched with 28 unique protein models predicted from C. lunatus m118 v.2 genome peptides. Furthermore, C. lunatus secreted peptides via classical and non-classical pathways related to virulence, proteolysis, nucleic acid metabolism, carbohydrate metabolism, heat stress, signal trafficking and some with unidentified catalytic domains.

CONCLUSIONS

We have identified a set of 5 soluble candidate effectors of unknown function from C. lunatus secretome weaponries against potato crop at different temperature regimes. Our findings demonstrate that C. lunatus has a repertoire of signature secretome which mediates thermo-pathogenicity and share a leucine rich "CL[xxxx]LHM"-motif. Considering the rapidly evolving temperature dependent-virulence and host diversity of C. lunatus, this data will be useful for designing new protection strategies.

Comparative proteomic analysis of differentially expressed proteins in the early milky stage of rice grains during high temperature stress

Rice yield and quality are adversely affected by high temperatures, and these effects are more pronounced at the 'milky stage' of the rice grain ripening phase. Identifying the functional proteins involved in the response of rice to high temperature stress may provide the basis for improving heat tolerance in rice. In the present study, a comparative proteomic analysis of paired, genetically similar heat-tolerant and heat-sensitive rice lines was conducted. Two-dimensional electrophoresis (2-DE) revealed a total of 27 differentially expressed proteins in rice grains, predominantly from the heat-tolerant lines. The protein profiles clearly indicated variations in protein expression between the heat-tolerant and heat-sensitive rice lines. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analysis revealed that 25 of the 27 differentially displayed proteins were homologous to known functional proteins. These homologous proteins were involved in biosynthesis, energy metabolism, oxidation, heat shock metabolism, and the regulation of transcription. Seventeen of the 25 genes encoding the differentially displayed proteins were mapped to rice chromosomes according to the co-segregating conditions between the simple sequence repeat (SSR) markers and the target genes in recombinant inbred lines (RILs). The proteins identified in the present study provide a basis to elucidate further the molecular mechanisms underlying the adaptation of rice to high temperature stress.

Proteomics analysis of alfalfa response to heat stress

The proteome responses to heat stress have not been well understood. In this study, alfalfa (Medicago sativa L. cv. Huaiyin) seedlings were exposed to 25°C (control) and 40°C (heat stress) in growth chambers, and leaves were collected at 24, 48 and 72 h after treatment, respectively. The morphological, physiological and proteomic processes were negatively affected under heat stress. Proteins were extracted and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE), and differentially expressed protein spots were identified by mass spectrometry (MS). Totally, 81 differentially expressed proteins were identified successfully by MALDI-TOF/TOF. These proteins were categorized into nine classes: including metabolism, energy, protein synthesis, protein destination/storage, transporters, intracellular traffic, cell structure, signal transduction and disease/defence. Five proteins were further analyzed for mRNA levels. The results of the proteomics analyses provide a better understanding of the molecular basis of heat-stress responses in alfalfa.

A comparative proteomic analysis of Pinellia ternata leaves exposed to heat stress

Pinellia ternata is an important traditional Chinese medicinal plant. The growth of P. ternata is sensitive to high temperatures. To gain a better understanding of heat stress responses in P. ternata, we performed a comparative proteomic analysis. P. ternata seedlings were subjected to a temperature of 38 °C and samples were collected 24 h after treatment. Increased relative ion leakage and lipid peroxidation suggested that oxidative stress was frequently generated in rice leaves exposed to high temperature. Two-dimensional electrophoresis (2-DE) was used to analyze heat-responsive proteins. More than 600 protein spots were reproducibly detected on each gel; of these spots, 20 were up-regulated, and 7 were down-regulated. A total of 24 proteins and protein species were successfully identified by MALDI-TOF/TOF MS. These proteins and protein species were found to be primarily small heat shock proteins (58%) as well as proteins involved in RNA processing (17%), photosynthesis (13%), chlorophyll biosynthetic processes (4%), protein degradation (4%) and defense (4%). Using 2-DE Western blot analysis, we confirmed the identities of the cytosolic class II small heat shock protein (sHSPs-CII) identified by MS. The expression levels of four different proteins [cytosolic class I small heat shock protein (sHSPs-CI), sHSPs-CII, mitochondrial small heat shock protein (sHSPs-MIT), glycine-rich RNA-binding protein (GRP)] were analyzed at the transcriptional level by quantitative real-time PCR. The mRNA levels of three sHSPs correlated with the corresponding protein levels. However, GRP was down-regulated at the beginning of heat stress but then increased substantially to reach a peak after 24 h of heat stress. Our study provides valuable new insight into the responses of P. ternata to heat stress.

Physiological and proteomic analyses of drought stress response in Holm oak provenances

Responses to drought stress by water withholding have been studied in 1 year old Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) seedlings from seven provenances from Andalusia (southern Spain). Several physiological parameters, including predawn xylem water potentials and relative water content in soil, roots, and leaves as well as maximum quantum efficiency and yield of PSII were evaluated for 28 days in both irrigated and nonirrigated seedlings. The leaf proteome map of the two provenances that show the extreme responses (Seville, GSE, is the most susceptible, while Almerı́a, SSA, is the least susceptible) was obtained. Statistically significant variable spots among provenances and treatments were subjected to MALDI-TOF/TOF-MS/MS analysis for protein identification. In response to drought stress, ~12.4% of the reproducible spots varied significantly depending on the treatment and the population. These variable proteins were mainly chloroplastic and belonged to the metabolism and defense/stress functional categories. The 2-DE protein profile of nonirrigated seedlings was similar in both provenances. Physiological and proteomics data were generally in good agreement. The general trend was a decrease in protein abundance upon water withholding in both provenances, mainly in those involved in ATP synthesis and photosynthesis. This decrease, moreover, was most marked in the most susceptible population compared with the less susceptible one.

Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom

BACKGROUND

Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling.

RESULTS

We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses.

CONCLUSION

In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined.

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade-offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.

Epigenetic regulation of adaptive responses of forest tree species to the environment

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.

Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus

High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥ 90%), thereby reducing the protein assignments into 7538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1432 protein groups that exhibited statistically significant (p ≤ 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quantitatively comparing a few proteins, a systems view of all the changes associated with a given cellular perturbation could be made.

The proteome of Populus nigra woody root: response to bending

BACKGROUND AND AIMS

Morphological and biomechanical alterations occurring in woody roots of many plant species in response to mechanical stresses are well documented; however, little is known about the molecular mechanisms regulating these important alterations. The first forest tree genome to be decoded is that of Populus, thereby providing a tool with which to investigate the mechanisms controlling adaptation of woody roots to changing environments. The aim of this study was to use a proteomic approach to investigate the response of Populus nigra woody taproot to mechanical stress.

METHODS

To simulate mechanical perturbations, the taproots of 30 one-year-old seedlings were bent to an angle of 90 ° using a steel net. A spatial and temporal two-dimensional proteome map of the taproot axis was obtained. We compared the events occurring in the above-bending, central bending and below-bending sectors of the taproot.

KEY RESULTS

The first poplar woody taproot proteome map is reported here; a total of 207 proteins were identified. Spatial and temporal proteomic analysis revealed that factors involved in plant defence, metabolism, reaction wood formation and lateral root development were differentially expressed in the various sectors of bent vs. control roots, seemingly in relation to the distribution of mechanical forces along the stressed woody taproots. A complex interplay among different signal transduction pathways involving reactive oxygen species appears to modulate these responses.

CONCLUSIONS

Poplar woody root uses different temporal and spatial mechanisms to respond to mechanical stress. Long-term bending treatment seem to reinforce the defence machinery, thereby enabling the taproot to better overcome winter and to be ready to resume growth earlier than controls.

Effects of heavy metals and arbuscular mycorrhiza on the leaf proteome of a selected poplar clone: a time course analysis

Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with the roots of most plant species. While receiving photosynthates, they improve the mineral nutrition of the plant and can also increase its tolerance towards some pollutants, like heavy metals. Although the fungal symbionts exclusively colonize the plant roots, some plant responses can be systemic. Therefore, in this work a clone of Populus alba L., previously selected for its tolerance to copper and zinc, was used to investigate the effects of the symbiosis with the AM fungus Glomus intraradices on the leaf protein expression. Poplar leaf samples were collected from plants maintained in a glasshouse on polluted (copper and zinc contaminated) or unpolluted soil, after four, six and sixteen months of growth. For each harvest, about 450 proteins were reproducibly separated on 2DE maps. At the first harvest the most relevant effect on protein modulation was exerted by the AM fungi, at the second one by the metals, and at the last one by both treatments. This work demonstrates how importantly the time of sampling affects the proteome responses in perennial plants. In addition, it underlines the ability of a proteomic approach, targeted on protein identification, to depict changes in a specific pattern of protein expression, while being still far from elucidating the biological function of each protein.

Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field

Water deficit affects tree growth and limits wood production. In an attempt to identify the molecular triggers of adaptation mechanisms to water deficit in Eucalyptus, we investigated protein expression patterns of two ecophysiologically contrasted Eucalyptus genotypes. They were grown in the field in either natural conditions or irrigated for 7 weeks during the dry season in the Republic of Congo. At the phenotypic level, genotype (G), treatment (T) and/or G × T interaction effects were observed for above- and below-ground biomass-related traits. At the molecular level, changes in protein abundance were recorded in leaves (acidic pH 4-7, and basic pH 7-11, proteomes) and stems (acidic proteome) using two-dimensional gel electrophoresis (2-DE). One third of the detected protein spots displayed significant G, T and/or G × T effects, and 158 of them were identified by tandem mass spectrometry (LC-MS/MS) analysis. Thus, several proteins whose molecular plasticity was genetically controlled (i.e. G × T effect) were revealed, highlighting adaptive mechanisms to water deficit specific to each genotype, namely cell wall modification, cell detoxification and osmoregulation. Transcript abundances corresponding to G × T proteins were also investigated by quantitative RT-PCR. These proteins represent relevant targets to improve drought resistance in this ecologically and economically important forest tree genus.

Microscopy and proteomic analysis of the non-host resistance of Oryza sativa to the wheat leaf rust fungus, Puccinia triticina f. sp. tritici

Rice (Oryza sativa) cv. Nipponbare expresses non-host resistance (NHR) to the wheat leaf rust fungus, Puccinia triticina f. sp. tritici (Ptt). When the leaves of cv. Nipponbare were inoculated with Ptt, approx 93% of the urediniospores germinated on the leaf surface, but only 10% of the germinated spores formed appressoria over the stomata at one day post inoculation (1 dpi). Hydrogen peroxide (H(2)O(2)) accumulated in host cells around the appressoria at 3 dpi. Approx. 3% of the appressoria produced short hyphae inside the leaf, and fluorescence was observed in tissue invaded by the hyphae by 7 dpi. At 22 dpi, 0.2% of the sites with appressoria formed branching infection hypha in mesophyll cells, but no substomatal vesicles, haustorial mother cells or haustoria were observed. Proteins were extracted from leaves 3 dpi and analyzed by two-dimensional gel electrophoresis (2-DE). A total 33 spots were reproducibly up-regulated and 9 were down-regulated by infection compared to the water inoculated control. Of these, 30 were identified by MALDI-TOF Mass Spectrometry. The identified proteins participate in defense/stress responses, energy/carbohydrate metabolism, oxidation-reduction processes, protein folding/turnover/cleavage/degradation, signal transduction and cell death regulation. The results indicates that NHR of rice to Ptt is consistent with a shift in protein and energy metabolism, increased antimicrobial activities, possibly including phytoalexin accumulation and cell wall reinforcement, increased cell repair, antioxidive and detoxification reactions, and enhanced prevention of plant cell death. Nearly half of the up-regulated identified proteins were associated with chloroplast and mitochondrial physiology suggesting important roles for these organelles during NHR.

Finding biomarkers is getting easier

Single biomarkers are rarely accurate. Even suites of biomarkers can give conflicting results. Ideally potent combinations of variables are isolated which accurately identify specific analytes and their level of toxicity. The search for such combinations can be done by reducing the thousands of candidate variables to the small number necessary for treatment classification. When the key variables are recognized by machine learning (ML) the results are quite surprising, given the apparent failure of other searching methods to produce good diagnostics. Proteins seem especially useful for portable field tests of a variety of adverse conditions. This review shows how ML, in particular artificial neural networks, can find potent biomarkers embedded in any type of expression data, mainly proteins in this article. A computer does multiple iterations to produce sets of proteins which systematically identify (to near 100% accuracy) the treatment classes of interest. Whether these proteins are useful in actual diagnoses is tested by presenting the computer model with unknown classes. Finding the biomarkers is getting easier but there still must be confirmation, by multivariable statistics and with field studies.