Proteomics of extreme freezing tolerance in Siberian spruce (Picea obovata)

Transcription factor DgMYB recruits H3K4me3 methylase to DgPEROXIDASE to enhance chrysanthemum cold tolerance

Cold affects the growth and development of plants. MYB transcription factors and histone H3K4me3 transferase ARABIDOPSIS TRITHORAXs (ATXs) play important regulatory functions in the process of plant resistance to low-temperature stress. In this study, DgMYB expression was responsive to low temperature, and overexpression of DgMYB led to increased tolerance, whereas the dgmyb mutant resulted in decreased tolerance of Chrysanthemum morifolium (Dendranthema grandiflorum var. Jinba) to cold stresses. Interestingly, we found that only peroxidase (POD) activity differed substantially between wild type (WT), overexpression lines, and the mutant line. A DgATX H3K4me3 methylase that interacts with DgMYB was isolated by further experiments. DgATX expression was also responsive to low temperature. Overexpression of DgATX led to increased tolerance, whereas the dgatx mutant resulted in decreased tolerance of chrysanthemum to cold stresses. Moreover, the dgmyb, dgatx, and dgmyb dgatx double mutants all led to reduced H3K4me3 levels at DgPOD, thus reducing DgPOD expression. Together, our results show that DgMYB interacts with DgATX, allowing DgATX to specifically target DgPOD, altering H3K4me3 levels, increasing DgPOD expression, and thereby reducing the accumulation of reactive oxygen species (ROS) in chrysanthemum.

Effects of drought stress memory on the accumulation of stress-protective compounds in naturally grown pine and spruce

Forest trees are subjected to multiple stressors during their long lifetime and therefore require effective and finely regulated stress-protective systems. Stressors can induce protective systems either directly or with the involvement of stress memory mechanisms. Stress memory has only begun to be uncovered in model plants and is unexplored in coniferous species. Therefore, we studied the possible role of stress memory in the regulation of the accumulation of stress-protective compounds (heat shock proteins, dehydrins, proline) in the needles of naturally grown Scots pine and Norway spruce trees subjected to the subsequent action of long-term (multiyear) and short-term (seasonal) water shortages. Although the water deficit was relatively mild, it significantly influenced the pattern of expression of stress memory-related heat shock factor (HSF) and SWI/SNF genes, indicating the formation of stress memory in both species. In spruce, dehydrin accumulation was increased by water shortage in a manner compatible with Type II stress memory. The accumulation of HSP40 in spruce needles was positively influenced by long-term water shortage, but this increase was unlikely to be of biological importance due to the concomitant decrease in HSP70, HSP90 and HSP101 accumulation. Finally, proline accumulation was negatively influenced by short-term water deficit in spruce. In pine, no one protective compound accumulated in response to water stress. Taken together, the results indicate that the accumulation of stress-protective compounds was generally independent of stress memory effects both in pine and in spruce.

Physiological and Proteomic Responses of Cassava to Short-Term Extreme Cool and Hot Temperature

Temperature is one of the most critical factors affecting cassava metabolism and growth. This research was conducted to investigate the effects of short-term exposure to extreme cool (15 °C) and hot (45 °C) temperature on photosynthesis, biochemical and proteomics changes in potted plants of two cassava cultivars, namely Rayong 9 and Kasetsart 50. One-month-old plants were exposed to 15, 30, and 45 °C for 60 min in a temperature chamber under light intensity of 700 μmol m⁻² s⁻¹. Compared to the optimum temperature (30 °C), exposure to 15 °C resulted in 28% reduction in stomatal conductance (gs) and 62% reduction in net photosynthesis rate (P_n). In contrast, gs under 45 °C increased 2.61 folds, while P_n was reduced by 50%. The lower P_n but higher electron transport rate (ETR) of the cold-stressed plants indicated that a greater proportion of electrons was transported via alternative pathways to protect chloroplast from being damaged by reactive oxygen species (ROS). Moreover, malondialdehyde (MDA) contents, a marker related to the amount of ROS, were significantly higher at low temperature. Proteomics analysis revealed some interesting differentially expressed proteins (DEPs) including annexin, a multi-functional protein functioning in early events of heat stress signaling. In response to low-temperature stress, AP2/ERF domain-containing protein (a cold-related transcription factor) and glutaredoxin domain-containing protein (a component of redox signaling network under cold stress) were detected. Taken together, both cultivars were more sensitive to low than high temperature. Moreover, Rayong 9 displayed higher P_n under both temperature stresses, and was more efficient in controlling ROS under cold stress than Kasetsart 50.

A natural antisense RNA improves chrysanthemum cold tolerance by regulating the transcription factor DgTCP1

Long noncoding RNAs (lncRNAs) are widely involved in the regulation of plant growth and development, but their mechanism of action in response to cold stress in plants remains unclear. Here, we found an lncRNA transcribed from the antisense strand of DgTCP1 (class I Teosinte branched1/Cycloidea/Proliferating [TCP] transcription factor) of chrysanthemum (Chrysanthemum morifolium Ramat.), named DglncTCP1. During the response of chrysanthemum to cold stress, overexpression of DgTCP1 improved the cold tolerance of chrysanthemum, while the DgTCP1 editing line (dgtcp1) showed decreased tolerance to cold stress. Overexpression of DglncTCP1 also increased the cold tolerance of chrysanthemum, while the DglncTCP1 amiRNA lines (DglncTCP1 amiR-18/38) also showed decreased tolerance to cold stress. Additionally, the overexpression of DglncTCP1 upregulated the expression of DgTCP1. This indicated that DglncTCP1 may play a cis-regulatory role in the regulatory process of DgTCP1 in cold tolerance. DglncTCP1 acts as a scaffold to recruit the histone modification protein DgATX (ARABIDOPSIS TRITHORAX from chrysanthemum) to DgTCP1 to enhance H3K4me3 levels, thereby activating DgTCP1 expression. Moreover, DgTCP1 can directly target DgPOD (peroxidase gene from chrysanthemum) to promote its expression and reduce reactive oxygen species accumulation, thereby improving the cold tolerance of chrysanthemum. In conclusion, these results suggest that natural antisense lncRNA plays a key role in improving the cold tolerance of chrysanthemum.

DgbZIP3 interacts with DgbZIP2 to increase the expression of DgPOD for cold stress tolerance in chrysanthemum

The bZIP transcription factor plays a very important role in abiotic stresses, e.g. drought, salt, and low-temperature stress, but the mechanism of action at low temperature is still unclear. In this study, overexpression of DgbZIP3 led to increased tolerance of chrysanthemum (Chrysanthemum morifolium Ramat.) to cold stress, whereas antisense suppression of DgbZIP3 resulted in decreased tolerance. Electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), luciferase complementary imaging analysis (LCI), and dual-luciferase reporter gene detection (DLA) experiments indicated that DgbZIP3 directly bound to the promoter of DgPOD and activated its expression. DgbZIP2 was identified as a DgbZIP3-interacting protein using yeast two-hybrid, co-immunoprecipitation, LCI, and bimolecular fluorescence complementation assays. Overexpression of DgbZIP2 led to increased tolerance of chrysanthemum to cold stress, whereas antisense suppression of DgbZIP2 resulted in decreased tolerance. A ChIP-qPCR experiment showed that DgbZIP2 was highly enriched in the promoter of DgPOD, while DLA, EMSA, and LCI experiments further showed that DgbZIP2 could not directly regulate the expression of DgPOD. The above results show that DgbZIP3 interacts with DgbZIP2 to regulate the expression of DgPOD to promote an increase in peroxidase activity, thereby regulating the balance of reactive oxygen species and improving the tolerance of chrysanthemum to low-temperature stress.

DgMYB2 improves cold resistance in chrysanthemum by directly targeting DgGPX1

MYB transcription factors play important roles in plant responses to cold stress, but the associated underlying mechanisms remain unclear. In this study, a cold-induced MYB transcription factor, DgMYB2, was isolated from chrysanthemum (Chrysanthemum morifolium Ramat). DgMYB2 was localized to the nucleus and exhibited transactivational activity. Overexpression of DgMYB2 improved cold tolerance in chrysanthemum, while cold tolerance in the antisense suppression lines decreased compared to that of the wild type. Additionally, electrophoretic mobility shift assays, chromatin immunoprecipitation, luciferase complementary imaging analysis, and dual-luciferase reporter gene detection experiments confirmed that DgMYB2 directly targets DgGPX1 and increases the activity of glutathione peroxidase to reduce the accumulation of reactive oxygen species, thereby improving cold resistance in chrysanthemum.

Lysine crotonylation of DgTIL1 at K72 modulates cold tolerance by enhancing DgnsLTP stability in chrysanthemum

Lysine crotonylation of proteins is a recently identified post-translational modification (PTM) in plants. However, the function of lysine-crotonylated proteins in response to abiotic stress in plants has not been reported. In this study, we identified a temperature-induced lipocalin-1-like gene (DgTIL1) from chrysanthemum and showed that it was notably induced in response to cold stress. Overexpression of DgTIL1 enhanced cold tolerance in transgenic chrysanthemum. Ubiquitin membrane yeast two-hybrid (MYTH) system and bimolecular fluorescence complementation (BIFC) assays showed that DgTIL1 interacts with a nonspecific lipid transfer protein (DgnsLTP), which can promote peroxidase (POD) gene expression and POD activity to reduce the accumulation of reactive oxygen species (ROS) and improve resistance to cold stress in DgnsLTP transgenic chrysanthemum. In addition, we found that DgTIL1 was lysine crotonylated at K72 in response to low temperature in chrysanthemum. Moreover, lysine crotonylation of DgTIL1 prevented DgnsLTP protein degradation in tobacco and chrysanthemum. Inhibition of DgnsLTP degradation by lysine crotonylation of DgTIL1 further enhanced POD expression and POD activity, reduced the accumulation of ROS under cold stress in DgTIL1 transgenic chrysanthemum, thus promoting the cold resistance of chrysanthemum.

Ectopic expression of human apolipoprotein D in Arabidopsis plants lacking chloroplastic lipocalin partially rescues sensitivity to drought and oxidative stress

The chloroplastic lipocalin (LCNP) is induced in response to various abiotic stresses including high light, dehydration and low temperature. It contributes to protection against oxidative damage promoted by adverse conditions by preventing accumulation of fatty acid hydroperoxides and lipid peroxidation. In contrast to animal lipocalins, LCNP is poorly characterized and the molecular mechanism by which it exerts protective effects during oxidative stress is largely unknown. LCNP is considered the ortholog of human apolipoprotein D (APOD), a protein whose lipid antioxidant function has been characterized. Here, we investigated whether APOD could functionally replace LCNP in Arabidopsis thaliana. We introduced APOD cDNA fused to a chloroplast transit peptide encoding sequence in an Arabidopsis LCNP KO mutant line and challenged the transgenic plants with different abiotic stresses. We demonstrated that expression of human APOD in Arabidopsis can partially compensate for the lack of the plastid lipocalin. The results are consistent with a conserved function of APOD and LCNP under stressful conditions. However, if the results obtained with the drought and oxidative stresses point to the protective effect of constitutive expression of APOD in plants lacking LCNP, this effect is not as effective as that conferred by LCNP overexpression. Moreover, when investigating APOD function in thylakoids after high light stress at low temperature, it appeared that APOD could not contribute to qH, a slowly reversible form of non-photochemical chlorophyll fluorescence quenching, as described for LCNP. This work provides a base of understanding the molecular mechanism underlying LCNP protective function.

Functional and morphological evolution in gymnosperms: A portrait of implicated gene families

Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.

Introduction: Plant Cold Acclimation and Winter Survival

This introductory chapter provides a brief overview of plant freezing tolerance, cold acclimation, including subzero acclimation, and the subsequent deacclimation when plants return to warm conditions favoring growth and development. We describe the basic concepts and approaches that are currently followed to investigate these phenomena. We highlight the multidisciplinary nature of these investigations and the necessity to use methodologies from different branches of science, such as ecology, genetics, physiology, cell biology, biochemistry, and biophysics to gain a complete understanding of the complex adaptive mechanisms ultimately underlying plant winter survival.

Remodeling of chloroplast proteome under salinity affects salt tolerance of Festuca arundinacea

Acclimation of photosynthetic apparatus to variable environmental conditions is an important component of tolerance to dehydration stresses, including salinity. The present study deals with the research on alterations in chloroplast proteome of the forage grasses. Based on chlorophyll fluorescence parameters, two genotypes of a model grass species-Festuca arundinacea with distinct levels of salinity tolerance: low salt tolerant (LST) and high salt tolerant (HST), were selected. Next, two-dimensional electrophoresis and mass spectrometry were applied under both control and salt stress conditions to identify proteins accumulated differentially between these two genotypes. The physiological analysis revealed that under NaCl treatment the studied plants differed in photosystem II activity, water content, and ion accumulation. The differentially accumulated proteins included ATPase B, ATP synthase, ribulose-1,5-bisphosphate carboxylase large and small subunits, cytochrome b6-f complex iron-sulfur subunit, oxygen-evolving enhancer proteins (OEE), OEE1 and OEE2, plastidic fructose-bisphosphate aldolase (pFBA), and lipocalin. A higher level of lipocalin, potentially involved in prevention of lipid peroxidation under stress, was also observed in the HST genotype. Our physiological and proteomic results performed for the first time on the species of forage grasses clearly showed that chloroplast metabolism adjustment could be a crucial factor in developing salinity tolerance.

Comparative proteomic analysis provides novel insights into chlorophyll biosynthesis in celery under temperature stress

Chlorophyll (Chl) is essential for light harvesting and energy transduction in photosynthesis. A proper amount of Chl within plant cells is important to celery (Apium graveolens) yield and quality. Temperature stress is an influential abiotic stress affecting Chl biosynthesis and plant growth. There are limited proteomic studies regarding Chl accumulation under temperature stress in celery leaves. Here, the proteins from celery leaves under different temperature treatments (4, 25 and 38°C) were analyzed using a proteomic approach. There were 71 proteins identified through MALDI-TOF-TOF analysis. The relative abundance of proteins involved in carbohydrate and energy metabolism, protein metabolism, amino acid metabolism, antioxidant and polyamine biosynthesis were enhanced under cold stress. These temperature stress-responsive proteins may establish a new homeostasis to enhance temperature tolerance. Magnesium chelatase (Mg-chelatase) and glutamate-1-semialdehyde aminotransferase (GSAT), related to Chl biosynthesis, showed increased abundances under cold stress. Meanwhile, the Chl contents were decreased in heat- and cold-stressed celery leaves. The inhibition of Chl biosynthesis may be due to the downregulated mRNA levels of 15 genes involved in Chl biosynthesis. The study will expand our knowledge on Chl biosynthesis and the temperature tolerance mechanisms in celery leaves.

Proteomic Changes Between Populus Allotriploids and Diploids Revealed Using an iTRAQ-based Quantitative Approach

Background

Polyploid breeding is a powerful approach for Populus genetic improve-ment because polyploid trees have valuable characteristics, including better timber quality and a higher degree of stress resistance compared with their full-sib diploids. However, the genetic mech-anism underlying this phenomenon remains unknown.

Objective

To better understand the proteomic changes between Populus allotriploids and diploids, we examined the proteomic profiles of allotriploid and diploid Populus by iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS).

Method

iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS).

Results

Between the Populus allotriploid and the full-sib diploid, 932 differentially expressed proteins (DEPs) were identified. These DEPs were primarily involved in stress, defense, transportation, transcriptional and/or translational modification, and energy production. The pathway analysis indi-cated that most of the DEPs were implicated in carbohydrate transport and metabolism, nitrogen me-tabolism and glycolysis, and the ribosome assembly pathway. These data suggest high protein di-vergence between Populus allotriploids and diploids, and rapid changes during hybridization.

Conclusion

The results provide new data for further understanding of the mechanisms of polyploid trees that generally display increased height growth compared with their full-sib diploids.

Fast acclimation of freezing resistance suggests no influence of winter minimum temperature on the range limit of European beech

Low temperature extremes drive species distribution at a global scale. Here, we assessed the acclimation potential of freezing resistance in European beech (Fagus sylvaticaL.) during winter. We specifically asked (i) how do beech populations growing in contrasting climates differ in their maximum freezing resistance, (ii) do differences result from genetic differentiation or phenotypic plasticity to preceding temperatures and (iii) is beech at risk of freezing damage in winter across its distribution range. We investigated the genetic and environmental components of freezing resistance in buds of adult beech trees from three different populations along a natural large temperature gradient in north-western Switzerland, including the site holding the cold temperature record in Switzerland. Freezing resistance of leaf primordia in buds varied significantly among populations, with LT50values (lethal temperature for 50% of samples) ranging from -25 to -40 °C, correlating with midwinter temperatures of the site of origin. Cambial meristems and the pith of shoots showed high freezing resistance in all three populations, with only a trend to lower freezing resistance at the warmer site. After hardening samples at -6 °C for 5 days, freezing resistance of leaf primordia increased in all provenances by up to 4.5 K. After additional hardening at -15 °C for 3 days, all leaf primordia were freezing resistant to -40 °C. We demonstrate that freezing resistance ofF. sylvaticahas a high ability to acclimate to temperature changes in winter, whereas the genetic differentiation of freezing resistance among populations seems negligible over this small geographic scale but large climatic gradient. In contrast to the assumption made in most of the species distribution models, we suggest that absolute minimum temperature in winter is unlikely to shape the cold range limit of beech. We conclude that the rapid acclimation of freezing resistance to winter temperatures allows beech to track changing climatic conditions, especially during unusually warm winters interrupted by very cold weather.

The Comparatively Proteomic Analysis in Response to Cold Stress in Cassava Plantlets

Cassava (Manihot esculenta Crantz) is a tropical root crop and sensitive to low temperature. However, it is poorly to know how cassava can modify its metabolism and growth to adapt to cold stress. An investigation aimed at a better understanding of cold-tolerant mechanism of cassava plantlets was carried out with the approaches of physiology and proteomics in the present study. The principal component analysis of seven physiological characteristics showed that electrolyte leakage (EL), chlorophyll content, and malondialdehyde (MDA) may be the most important physiological indexes for determining cold-resistant abilities of cassava. The genome-wide proteomic analysis showed that 20 differential proteins had the same patterns in the apical expanded leaves of cassava SC8 and Col1046. They were mainly related to photosynthesis, carbon metabolism and energy metabolism, defense, protein synthesis, amino acid metabolism, signal transduction, structure, detoxifying and antioxidant, chaperones, and DNA-binding proteins, in which 40 % were related with photosynthesis. The remarkable variation in photosynthetic activity and expression level of peroxiredoxin is closely linked with expression levels of proteomic profiles. Moreover, analysis of differentially expressed proteins under cold stress is an important step toward further elucidation of mechanisms of cold stress resistance.

The cold responsive mechanism of the paper mulberry: decreased photosynthesis capacity and increased starch accumulation

Background

Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to cold stress in this study.

Methods

The second to fourth fully expanded leaves from up to down were harvested at different stress time points forthe transmission electron microscope (TEM) observation. Physiological characteristics measurement included the relative electrolyte leakage (REL), SOD activity assay, soluble sugar content, and Chlorophyll fluorescence parameter measurement. For screening of differentially expressed genes, the expression level of every transcript in each sample was calculated by quantifying the number of Illumina reads. To identify the differentially expressed protein, leaves of plants under 0, 6, 12, 24, 48 and 72 h cold stress wereharvested for proteomic analysis. Finally, real time PCR was used to verify the DEG results of the RNA-seq and the proteomics data.

Results

Results showed that at the beginning of cold stress, respiratory metabolism was decreased and the transportation and hydrolysis of photosynthetic products was inhibited, leading to an accumulation of starch in the chloroplasts. Total of 5800 unigenes and 38 proteins were affected, including the repressed expression of photosynthesis and the enhanced expression in signal transduction, stress defense pathway as well as secondary metabolism. Although the transcriptional level of a large number of genes has been restored after 12 h, sustained cold stress brought more serious injury to the leaf cells, including the sharp rise of the relative electrolyte leakage, the declined Fv/Fm value, swelled chloroplast and the disintegrated membrane system.

Conclusion

The starch accumulation and the photoinhibition might be the main adaptive mechanism of the paper mulberry responded to cold stress. Most of important, enhancing the transport and hydrolysis of photosynthetic products could be the potential targets for improving the cold tolerance of the paper mulberry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2047-6) contains supplementary material, which is available to authorized users.

Seasonal changes in the content of dehydrins in mesophyll cells of common pine needles

The appearance of dehydrins (DHNs) in cells is required for the development of cold resistance. DHNs are therefore considered specific markers of cold resistance by some authors. DHNs accumulate in plants concomitantly with a reduction of intracellular water content, and presumably protect membranes and proteins from damage caused by moisture loss. DHN content in pine needles increases in spring and autumn when moisture availability and temperatures are most unfavorable. The present work is focused on seasonal changes in DHN content in various mesophyll-cell compartments of pine (Pinus sylvestris L.) needles in association with changes in environmental factors. In spring, the number of thylakoid membranes per granum was lower than in summer and autumn. An increase in needle content of DHNs with approximate masses of 76, 73, 72, 35, and 17 kD in spring and autumn, associated with needle dehydration during this period, is shown here. The largest increase in DHN content was observed in spring, with the highest amount of DHNs presented in chloroplast membrane system including grana thylakoids, stromal thylakoids, and the two chloroplast envelope membranes and in cell walls. In the autumn, most DHNs were localized in chloroplasts and mitochondria.

Biogenesis of mitochondria in cauliflower (Brassica oleracea var. botrytis) curds subjected to temperature stress and recovery involves regulation of the complexome, respiratory chain activity, organellar translation and ultrastructure

The biogenesis of the cauliflower curd mitochondrial proteome was investigated under cold, heat and the recovery. For the first time, two dimensional fluorescence difference gel electrophoresis was used to study the plant mitochondrial complexome in heat and heat recovery. Particularly, changes in the complex I and complex III subunits and import proteins, and the partial disintegration of matrix complexes were observed. The presence of unassembled subunits of ATP synthase was accompanied by impairment in mitochondrial translation of its subunit. In cold and heat, the transcription profiles of mitochondrial genes were uncorrelated. The in-gel activities of respiratory complexes were particularly affected after stress recovery. Despite a general stability of respiratory chain complexes in heat, functional studies showed that their activity and the ATP synthesis yield were affected. Contrary to cold stress, heat stress resulted in a reduced efficiency of oxidative phosphorylation likely due to changes in alternative oxidase (AOX) activity. Stress and stress recovery differently modulated the protein level and activity of AOX. Heat stress induced an increase in AOX activity and protein level, and AOX1a and AOX1d transcript level, while heat recovery reversed the AOX protein and activity changes. Conversely, cold stress led to a decrease in AOX activity (and protein level), which was reversed after cold recovery. Thus, cauliflower AOX is only induced by heat stress. In heat, contrary to the AOX activity, the activity of rotenone-insensitive internal NADH dehydrogenase was diminished. The relevance of various steps of plant mitochondrial biogenesis to temperature stress response and recovery is discussed.

Plant cold acclimation and freezing tolerance

This introductory chapter provides a brief overview of plant freezing tolerance and cold acclimation and describes the basic concepts and approaches that are currently followed to investigate these phenomena. We highlight the multidisciplinary nature of these investigations and the necessity to use methodologies from different branches of science, such as ecology, genetics, physiology, biochemistry, and biophysics, to come to a complete understanding of the complex adaptive mechanisms underlying plant cold acclimation.

Extreme low temperature tolerance in woody plants

Woody plants in boreal to arctic environments and high mountains survive prolonged exposure to temperatures below -40°C and minimum temperatures below -60°C, and laboratory tests show that many of these species can also survive immersion in liquid nitrogen at -196°C. Studies of biochemical changes that occur during acclimation, including recent proteomic and metabolomic studies, have identified changes in carbohydrate and compatible solute concentrations, membrane lipid composition, and proteins, notably dehydrins, that may have important roles in survival at extreme low temperature (ELT). Consideration of the biophysical mechanisms of membrane stress and strain lead to the following hypotheses for cellular and molecular mechanisms of survival at ELT: (1) Changes in lipid composition stabilize membranes at temperatures above the lipid phase transition temperature (-20 to -30°C), preventing phase changes that result in irreversible injury. (2) High concentrations of oligosaccharides promote vitrification or high viscosity in the cytoplasm in freeze-dehydrated cells, which would prevent deleterious interactions between membranes. (3) Dehydrins bind membranes and further promote vitrification or act stearically to prevent membrane-membrane interactions.

Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)

Siberian spruce (Picea obovata) is one of several boreal conifer species that can survive at extremely low temperatures (ELTs). When fully acclimated, its tissues can survive immersion in liquid nitrogen. Relatively little is known about the biochemical and biophysical strategies of ELT survival. We profiled needle metabolites using gas chromatography coupled with mass spectrometry (GC-MS) to explore the metabolic changes that occur during cold acclimation caused by natural temperature fluctuations. In total, 223 metabolites accumulated and 52 were depleted in fully acclimated needles compared with pre-acclimation needles. The metabolite profiles were found to develop in four distinct phases, which are referred to as pre-acclimation, early acclimation, late acclimation and fully acclimated. Metabolite changes associated with carbohydrate and lipid metabolism were observed, including changes associated with increased raffinose family oligosaccharide synthesis and accumulation, accumulation of sugar acids and sugar alcohols, desaturation of fatty acids, and accumulation of digalactosylglycerol. We also observed the accumulation of protein and nonprotein amino acids and polyamines that may act as compatible solutes or cryoprotectants. These results provide new insight into the mechanisms of freezing tolerance development at the metabolite level and highlight their importance in rapid acclimation to ELT in P. obovata.

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).

Temperature-induced lipocalin (TIL) is translocated under salt stress and protects chloroplasts from ion toxicity

Temperature-induced lipocalins (TIL) have been invoked in the defense from heat, cold and oxidative stress. Here we document a function of TIL for basal protection from salinity stress. Heterologous expression of TIL from the salt resistant poplar Populus euphratica did not rescue growth but prevented chlorophyll b destruction in salt-exposed Arabidopsis thaliana. The protein was localized to the plasma membrane but was re-translocated to the symplast under salt stress. The A. thaliana knock out and knock down lines Attil1-1 and Attil1-2 showed stronger stress symptoms and stronger chlorophyll b degradation than the wildtype (WT) under excess salinity. They accumulated more chloride and sodium in chloroplasts than the WT. Chloroplast chloride accumulation was found even in the absence of salt stress. Since lipocalins are known to bind regulatory fatty acids of channel proteins as well as iron, we suggest that the salt-induced trafficking of TIL may be required for protection of chloroplasts by affecting ion homeostasis.

Arabidopsis lipocalins AtCHL and AtTIL have distinct but overlapping functions essential for lipid protection and seed longevity

Lipocalins are a group of multifunctional proteins, recognized as carriers of small lipophilic molecules, which have been characterized in bacteria and animals. Two true lipocalins have been recently identified in plants, the temperature-induced lipocalin (TIL) and the chloroplastic lipocalin (CHL), the expression of which is induced by various abiotic stresses. Each lipocalin appeared to be specialized in the responses to specific stress conditions in Arabidopsis thaliana, with AtTIL and AtCHL playing a protective role against heat and high light, respectively. The double mutant AtCHL KO × AtTIL KO deficient in both lipocalins was more sensitive to temperature, drought and light stresses than the single mutants, exhibiting intense lipid peroxidation. AtCHL deficiency dramatically enhanced the photosensitivity of mutants (vte1, npq1) affected in lipid protection mechanisms (tocopherols, zeaxanthin), confirming the role of lipocalins in the prevention of lipid peroxidation. Seeds of the AtCHL KO × AtTIL KO double mutant were very sensitive to natural and artificial ageing, and again this phenomenon was associated with the oxidation of polyunsaturated lipids. The presented results show that the Arabidopsis lipocalins AtTIL and AtCHL have overlapping functions in lipid protection which are essential for stress resistance and survival.

Dehydrin accumulation and extreme low-temperature tolerance in Siberian spruce (Picea obovata)

To investigate the role of dehydrins (DHNs) in extreme low-temperature (LT) tolerance, we sampled needle tissue of Siberian spruce (Picea obovata Ledeb.) from trees growing in an arboretum in Trondheim, Norway from August 2006 to April 2007 and tracked changes in LT tolerance via relative electrolyte leakage. We used western blotting to estimate relative amounts of proteins binding a DHN K-segment antibody, measured relative amounts of nine transcripts for small (<25 kDa) DHNs by quantitative reverse transcription-polymerase chain reaction (PCR) using primers developed for DHN transcripts in a closely related species, Picea abies (L.) Karsten, and isolated and sequenced PCR products for five P. obovata DHNs. Three protein bands of 53, 35 and 33 kDa were detected on western blots of SDS-PAGE-separated protein extracts. The 53-kDa DHN was already present late in the growing season, but accumulated during acclimation, and levels decreased rapidly during deacclimation. The 33- and 35-kDa proteins, identified as Picg5 class DHNs by mass spectrometry, first appeared in detectable amounts late in the acclimation process and remained at detectable levels throughout the period of maximum LT tolerance. Levels of the 53-kDa DHN correlated with two LT tolerance parameters, while results for the 33- and 35-kDa proteins were equivocal due to limited sample size and variation in LT tolerance during the mid-winter period. Three additional bands of 30, 28 and 26 kDa were detected in extracts from needles collected in November 2010 using an immunity-purified antibody. Immunoblotting of two-dimensional gel electrophoresis gels loaded with proteins extracted from October and November samples corroborated the results obtained by SDS-PAGE western blots. One large spot in the 53 kDa range and two trains of spots in the same size range as the 33 and 35 kDa DHNs were detected using the K-segment antibody. Eight of the nine DHN transcripts closely tracked LT tolerance parameters, whereas the ninth DHN transcripts followed a reverse pattern, decreasing during winter and increasing again during deacclimation. Multiple regression models using principal components of the transcripts to predict two different LT tolerance parameters suggest separate but overlapping functions for different DHNs in establishing and maintaining extreme LT tolerance.

Nitric oxide-cold stress signalling cross-talk, evolution of a novel regulatory mechanism

Plants enhance their cold stress tolerance by cold acclimation, a process which results in vast reprogramming of transcriptome, proteome and metabolome. Evidence suggests nitric oxide (NO) production during cold stress which regulates genes (especially the C-repeat binding factor (CBF) cold stress signalling pathway), diverse proteins including transcription factors (TFs) and phosphosphingolipids. About 59% (redox), 50% (defence/stress) and 30% (signalling) cold responsive proteins are modulated by NO-based post translational modifications (PTMs) namely S-nitrosylation, tyrosine nitration and S-glutathionylation, suggesting a cross-talk between NO and cold. Analysis of cold stress responsive deep proteome in apoplast, mitochondria, chloroplast and nucleus suggested continuation of this cross-talk in sub-cellular systems. Modulation of cold responsive proteins by these PTMs right from cytoskeletal elements in plasma membrane to TFs in nucleus suggests a novel regulation of cold stress signalling. NO-mediated altered protein transport in nucleus seems an important stress regulatory mechanism. This review addresses the NO and cold stress signalling cross-talk to present the overview of this novel regulatory mechanism.

Proteins involved in distinct phases of cold hardening process in frost resistant winter barley (Hordeum vulgare L.) cv Luxor

Winter barley is an economically important cereal crop grown in higher latitudes and altitudes where low temperatures represent an important environmental constraint limiting crop productivity. In this study changes in proteome of leaves and crowns in a frost tolerant winter barley cv. Luxor in relation to short and long term periods of cold followed by a brief frost treatment were studied in order to disclose proteins responsible for the cold hardening process in distinct plant tissues. The mentioned changes have been monitored using two dimensional difference gel electrophoresis (2D-DIGE) with subsequent peptide-mapping protein identification. Regarding approximately 600–700 distinct protein spots detected on 2D gels, there has been found at least a two-fold change after exposure to low temperatures in about 10% of proteins in leaves and 13% of proteins in crowns. Protein and nitrogen metabolic processes have been influenced by low temperature to a similar extent in both tissues while catabolism, carbohydrate metabolism and proteins involved in stress response have been more affected in crowns than in leaves. The range of changes in protein abundance was generally higher in leaves and chloroplast proteins were frequently affected which suggests a priority to protect photosynthetic apparatus. Overall, our data proved existence of slightly different response strategies to low temperature stress in crowns and leaves, i.e., tissues with different biological role. Moreover, there have been found several proteins with large increase in accumulation, e.g., 33 kDa oxygen evolving protein of photosystem II in leaves and “enhanced disease susceptibility 1” in crowns; these proteins might have potential to indicate an enhanced level of frost tolerance in barley.

Investigation of glandular trichome proteins in Artemisia annua L. using comparative proteomics

Glandular secreting trichomes (GSTs) are called biofactories because they are active in synthesizing, storing and secreting various types of plant secondary metabolites. As the most effective drug against malaria, artemisinin, a sesquiterpene lactone is derived from GSTs of Artemisia annua. However, low artemisinin content (0.001%∼1.54% of dry weight) has hindered its wide application. We investigate the GST-expressed proteins in Artemisia annua using a comparative proteomics approach, aiming for a better understanding of the trichome proteome and arteminisin metabolism. 2D-electrophoresis was employed to compare the protein profiles of GSTs and leaves. More than 700 spots were resolved for GSTs, of which ∼93 non-redundant proteins were confidently identified by searching NCBI and Artemisia EST databases. Over 70% of these proteins were highly expressed in GTSs. Functional classification of these GSTs enriched proteins revealed that many of them participate in major plant metabolic processes such as electron transport, transcription and translation.

Molecular interactions between the olive and the fruit fly Bactrocera oleae

BACKGROUND

The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively.

RESULTS

We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures.

CONCLUSIONS

This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.

Metabolite profiling reveals novel multi-level cold responses in the diploid model Fragaria vesca (woodland strawberry)

Winter freezing damage is a crucial factor in overwintering crops such as the octoploid strawberry (Fragaria × ananassa Duch.) when grown in a perennial cultivation system. Our study aimed at assessing metabolic processes and regulatory mechanisms in the close-related diploid model woodland strawberry (Fragaria vescaL.) during a 10-days cold acclimation experiment. Based on gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS) metabolite profiling of three F. vesca genotypes, clear distinctions could be made between leaves and non-photosynthesizing roots, underscoring the evolvement of organ-dependent cold acclimation strategies. Carbohydrate and amino acid metabolism, photosynthetic acclimation, and antioxidant and detoxification systems (ascorbate pathway) were strongly affected. Metabolic changes in F. vesca included the strong modulation of central metabolism, and induction of osmotically-active sugars (fructose, glucose), amino acids (aspartic acid), and amines (putrescine). In contrast, a distinct impact on the amino acid proline, known to be cold-induced in other plant systems, was conspicuously absent. Levels of galactinol and raffinose, key metabolites of the cold-inducible raffinose pathway, were drastically enhanced in both leaves and roots throughout the cold acclimation period of 10 days. Furthermore, initial freezing tests and multifaceted GC/TOF-MS data processing (Venn diagrams, independent component analysis, hierarchical clustering) showed that changes in metabolite pools of cold-acclimated F. vesca were clearly influenced by genotype.

Proteomics research on forest trees, the most recalcitrant and orphan plant species

The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.

Proteome analysis of cold acclimation in sunflower

Cold acclimation is the phenomenon in which plants are exposed to low, but nonfreezing, temperatures before exposure to drastic temperatures. To investigate how sunflower plants adjust their metabolism during cold treatment, a comparative proteomic approach, based on spectral counting data, was adopted to identify differentially expressed proteins in leaves of freezing susceptible (Hopi) and tolerant (PI 543006 and BSD-2-691) lines after cold acclimation. In total 718, 675, and 769 proteins were confidently identified by tandem mass spectrometry in Hopi, PI 543006, and BSD-2-691 sunflower lines. Tolerant lines PI 543006 and BSD-2-691 showed the highest number of differentially expressed proteins, as 43, 72, and 168 proteins changed their expression in Hopi, PI 543006, and BSD-2-691 sunflower lines, respectively, at 95% confidence. Cold-responsive proteins were mostly involved in metabolism, protein synthesis, energy, and defense processes in all sunflower lines studied. Hierarchical clustering of all differentially expressed proteins resulted in the characterization of 14 different patterns of expression across Hopi, PI 543006, and BSD-2-691 and indicated that tolerant lines showed different proteome responses to cold acclimation.