A global survey of gene regulation during cold acclimation in Arabidopsis thaliana

Many temperate plant species such as Arabidopsis thaliana are able to increase their freezing tolerance when exposed to low, nonfreezing temperatures in a process called cold acclimation. This process is accompanied by complex changes in gene expression. Previous studies have investigated these changes but have mainly focused on individual or small groups of genes. We present a comprehensive statistical analysis of the genome-wide changes of gene expression in response to 14 d of cold acclimation in Arabidopsis, and provide a large-scale validation of these data by comparing datasets obtained for the Affymetrix ATH1 Genechip and MWG 50-mer oligonucleotide whole-genome microarrays. We combine these datasets with existing published and publicly available data investigating Arabidopsis gene expression in response to low temperature. All data are integrated into a database detailing the cold responsiveness of 22,043 genes as a function of time of exposure at low temperature. We concentrate our functional analysis on global changes marking relevant pathways or functional groups of genes. These analyses provide a statistical basis for many previously reported changes, identify so far unreported changes, and show which processes predominate during different times of cold acclimation. This approach offers the fullest characterization of global changes in gene expression in response to low temperature available to date.     

Expression of a cold-responsive Lt-Cor gene and development of freezing tolerance during cold acclimation in wheat (Triticum aestivum L.).

Time-courses of the development of freezing tolerance and the expression of a cold-responsive gene wlt10 were monitored during cold acclimation in wheat (Triticum aestivum L.). Bioassay showed that cold acclimation conferred much higher freezing tolerance on a winter cultivar than a spring cultivar. Northern blot analysis showed that the expression of wlt10 encoding a novel wheat member of a cereal-specific LT-COR protein family was specifically induced by low temperature. A freezing-tolerant winter cultivar accumulated the mRNA more rapidly and for a longer period than a susceptible spring cultivar. The increase in the amount of mRNA was temporary but the peak occurred at the time when the maximum level of freezing tolerance was attained. The mRNA accumulated more in the leaves than in the roots, and different light/dark regimes modulated the level of mRNA accumulation. Genomic Southern blot analyses using the nulli-tetrasomic series showed that the wlt10 homologues were located on the homologous group 2 chromosomes.     

Impaired chloroplast positioning affects photosynthetic capacity and regulation of the central carbohydrate metabolism during cold acclimation

Photosynthesis Research - Photosynthesis and carbohydrate metabolism of higher plants need to be tightly regulated to prevent tissue damage during environmental changes. The intracellular position...     

A novel plant defensin-like gene of winter wheat is specifically induced during cold acclimation

A novel cDNA clone, Tad1, was isolated from crown tissue of winter wheat after differential screening of cold acclimation-induced genes. The Tad1 cDNA encoded a 23kDa polypeptide with a potential N-terminal signal sequence. The putative mature sequence showed striking similarity to plant defensins or gamma-thionins, representing low molecular size antipathogenic polypeptides. High levels of Tad1 mRNA accumulation occurred within one day of cold acclimation in crown tissue and the level was maintained throughout 14 days of cold acclimation. Similar rapid induction was observed in young seedlings treated with low temperature but not with exogenous abscisic acid. In contrast to defensins from other plant species, neither salicylic acid nor methyl jasmonate induced expression of Tad1. The recombinant mature form of TAD1 polypeptide inhibited the growth of the phytopathogenic bacteria, Pseudomonas cichorii; however, no antifreeze activity was detected. Collectively, these data suggested that Tad1 is induced in cold-acclimated winter wheat independent of major defense signaling(s) and is involved in low temperature-induced resistance to pathogens during winter hardening.     

Energy metabolism, thermogenesis and body mass regulation in Brandt's voles (Lasiopodomys brandtii) during cold acclimation and rewarming

Environmental cues play important roles in the regulation of an animal's physiology and behavior. The purpose of the present study was to test the hypothesis that ambient temperature was a cue to induce adjustments in body mass, energy intake and thermogenic capacity, associated with changes in serum leptin levels in Brandt's voles (Lasiopodomys brandtii). We found that Brandt's voles increased resting metabolic rate (RMR) and energy intake and kept body mass stable when exposed to the cold while showed a significant increase in body mass after rewarming. The increase in body mass after rewarming was associated with the higher energy intake compared with control. Uncoupling protein 1 (UCP1) content in brown adipose tissue (BAT) increased in the cold and reversed after rewarming. Serum leptin levels decreased in the cold while increased after rewarming, associated with the opposite changes in energy intake. Further, serum leptin levels were positively correlated with body mass and body fat mass. Together, these data supported our hypothesis that ambient temperature was a cue to induce changes in body mass and metabolism. Serum leptin, as a starvation signal in the cold and satiety signal in rewarming, was involved in the processes of thermogenesis and body mass regulation in Brandt's voles.     

A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis

Low temperatures lead to the inhibition of sucrose synthesis and photosynthesis. The biochemical and physiological adaptations of plants to low temperatures include the post-translational activation and increased expression of enzymes of the sucrose synthesis pathway, the changed expression of Calvin cycle enzymes, and changes in the leaf protein content. Recent progress has been made in understanding both the signals that trigger these processes and how the regulation of photosynthetic carbon metabolism interacts with other processes during cold acclimation.     

Body temperature regulation during acclimation to cold and hypoxia in rats

Extreme environmental conditions present challenges for thermoregulation in homoeothermic organisms such as mammals. Such challenges are exacerbated when two stressors are experienced simultaneously and each stimulus evokes opposing physiological responses. This is the case of cold, which induces an increase in thermogenesis, and hypoxia, which suppresses metabolism conserving oxygen and preventing hypoxaemia. As an initial approach to understanding the thermoregulatory responses to cold and hypoxia in a small mammal, we explored the effects of acclimation to these two stressors on the body temperature (T_b) and the daily and ultradian T_b variations of Sprague-Dawley rats. As T_b is influenced by sleep-wake cycles, these T_b variations reflect underlying adjustments in set-point and thermosensitivity. The T_b of rats decreased precipitously during initial hypoxic exposure which was more pronounced in cold (T_b=33.4±0.13) than in room temperature (T_b=35.74±0.17) conditions. This decline was followed by an increase in T_b stabilising at a new level ~0.5 °C and ~1.4 °C below normoxic values at room and cold temperatures, respectively. Daily T_b variations were blunted during hypoxia with a greater effect in the cold. Ultradian T_b variations exhibited daily rhythmicity that disappeared under hypoxia, independent of ambient temperature. The adjustments in T_b during hypoxia and/or cold are in agreement with the hypothesis that an initial decrease in the T_b set-point is followed by its partial re-establishment with chronic hypoxia. This rebound of the T_b set-point might reflect cellular adjustments that would allow animals to better deal with low oxygen conditions, diminishing the drive for a lower T_b set-point. Cold and hypoxia are characteristic of high altitude environments. Understanding how mammals cope with changes in oxygen and temperature will shed light into their ability to colonize new environments along altitudinal clines and increase our understanding of how T_b is regulated under stimuli that impose contrasting physiological constraints.     

Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana

Metabolite changes in plant leaves during exposure to low temperatures involve re‐allocation of a large number of metabolites between sub‐cellular compartments. Therefore, metabolite determination at the whole cell level may be insufficient for interpretation of the functional significance of cellular compounds. To investigate the cold‐induced metabolite dynamics at the level of individual sub‐cellular compartments, an integrative platform was developed that combines quantitative metabolite profiling by gas chromatography coupled to mass spectrometry (GC‐MS) with the non‐aqueous fractionation technique allowing separation of cytosol, vacuole and the plastidial compartment. Two mutants of Arabidopsis thaliana representing antipodes in the diversion of carbohydrate metabolism between sucrose and starch were compared to Col‐0 wildtype before and after cold acclimation to investigate interactions of cold acclimation with subcellular re‐programming of metabolism. A multivariate analysis of the data set revealed dominant effects of compartmentation on metabolite concentrations that were modulated by environmental condition and genetic determinants. While for both, the starchless mutant of plastidial phospho‐gluco mutase (pgm) and a mutant defective in sucrose‐phosphate synthase A1, metabolic constraints, especially at low temperature, could be uncovered based on subcellularly resolved metabolite profiles, only pgm had lowered freezing tolerance. Metabolic profiles of pgm point to redox imbalance as a possible reason for reduced cold acclimation capacity.     

Energy metabolism, thermogenesis and body mass regulation in tree shrew (Tupaia belangeri) during subsequent cold and warm acclimation

Environmental cues play important roles in the regulation of an animal's physiology and behavior. The purpose of the present study was to test the hypothesis that ambient temperature is a cue to induce adjustments in body mass, energy intake and thermogenic capacity, associated with changes in serum leptin levels in tree shrews (Tupaia belangeri). We found that tree shrews increased basal metabolic rate (BMR), energy intake and subsequently showed a significant decrease in body mass after being returned to warm ambient temperature. Uncoupling protein 1 (UCP1) content in brown adipose tissue (BAT) increased during cold acclimation and reversed after rewarming. The trend of energy intake increased during cold acclimation and decreased after rewarming; the trend of energy intake during cold acclimation was contrary to the trend of energy intake during rewarming. Further, serum leptin levels were negatively correlated with body mass. Together, these data supported our hypothesis that ambient temperature was a cue to induce changes in body mass and metabolic capacity. Serum leptin, as a starvation signal in the cold and satiety signal in rewarming, was involved in the processes of thermogenesis and body mass regulation in tree shrews.     

冷驯化条件下大绒鼠的产热和能量代谢特征

本文主要研究了冷驯化(5℃±1℃)条件下,大绒鼠(Eothenomys miletus)的能量收支、基础代谢率(BMR)、非颤抖性产热(NST)和肝脏线粒体呼吸.结果表明:随着冷驯化的进行,大绒鼠的体重、体温降低;摄入能、消化能、可代谢能增加;BMR和NST增加;肝脏线粒体呼吸状态Ⅲ呼吸先增加,28天后趋于平稳;线粒体状态Ⅳ呼吸先增加,28天后下降.说明在冷驯化条件下,大绒鼠采取适当降低体重和体温、增加能量摄入、增加BMR和NST产热的对策来维持能量平衡     

Dynamic compositional changes of detergent-resistant plasma membrane microdomains during plant cold acclimation

Plants increase their freezing tolerance upon exposure to low, non-freezing temperatures, which is known as cold acclimation. Cold acclimation results in a decrease in the proportion of sphingolipids in the plasma membrane in many plants including Arabidopsis thaliana. The decrease in sphingolipids has been considered to contribute to the increase in the cryostability of the plasma membrane through regulating membrane fluidity. Recently we have proposed a possibility of another important sphingolipid function associated with cold acclimation.¹ In animal cells, it has been known that the plasma membrane contains microdomains due to the characteristics of sphingolipids and sterols, and the sphingolipid- and sterol-enriched microdomains are thought to function as platforms for cell signaling, membrane trafficking and pathogen response. In our research on characterization of microdomain-associated lipids and proteins in Arabidopsis, a cold-acclimation-induced decrease in sphingolipids resulted in a decrease of microdomains in the plasma membrane and there were considerable changes in membrane transport-, cytoskeleton- and endocytosis-related proteins in the microdomains during cold acclimation. Based on these results, we discuss a functional relationship between the changes in microdomain components and plant cold acclimation.Key words: Arabidopsis, cold acclimation, detergent-resistant plasma membrane, plasma membrane lipid, plasma membrane protein, microdomain, proteome analysisIn fall or early winter, plants recognize the decrease in temperature and change cellular metabolism to survive against freezing stress. This phenomenon is termed as cold acclimation.² Because the plasma membrane is the critical site in cell survival during freezing, diverse cold-acclimation-induced changes are believed to ultimately protect the plasma membrane from the irreversible damage under freezing stress.³ One of the notable changes during cold acclimation is a decrease in sphingolipids, a characteristic plasma membrane lipid.⁴ Sphingolipids have melting temperatures higher than do phosphsolipids, major plasma membrane lipids. Thus, quantitative decreases in sphonglipids are considered to increase in membrane fluidity at low temperatures.⁴ Some 20 years ago, however, experimental results that sphinglipids form lipid microdomains in the plasma membrane were reported in mammalian and yeast cells.^5–7 Sphingolipids are heterogeneously distributed and self-associated with sterols and specific proteins in the plasma membrane. The sphingolipid/sterol-enriched microdomains in the plasma membrane are sometime called “membrane (lipid) raft” or “caveolae” in mammalian cells, and similar domains have been proposed later in plant cells.^8–11 The microdomains are biochemically isolated as low-density detergent-resistant plasma membrane (DRM) fractions and contain specific proteins associated with membrane trafficking, signal transduction, membrane transport, cytoskeleton interaction and pathogen infection.¹² Consequently, the microdomains are suspected to function as platform for assembly of these functional protein complexes and temporal interaction between protein-protein or protein-lipid.⁷ The microdomains change not only in domain size by coalescence of individual domains but also in protein and lipid compositions by physiological stimulus.^12–15We hypothesized that a decrease of sphingolipids in the plant plasma membrane during cold acclimation might not only increase membrane fluidity but also change microdomain formation and/or function. Our recent paper characterized cold-responsiveness of lipid and protein components in plant DRMs.¹ Arabidopsis thaliana is able to increase in freezing tolerance after few days of cold treatment [the temperature of 50% survival is −7°C before cold treatment at 2°C and decreases to −15°C after 7-d-treatment]. We first isolated plasma membrane-enriched fractions using aqueous two-phase partition system from Arabidopsis seedlings before and after cold acclimation. Next, plasma membrane fractions were subjected to 1% (w/v) Triton X-100 on ice for 30 min and then sucrose density gradient centrifugation. DRM fractions appeared as two white bands at about 40% (w/w) sucrose. DRMs in plants are generally recovered as heavier fractions than those in animals.^16–18 This is probably because the ratio of protein to lipid is greater in plants than in animals. Arabidopsis DRM fractions were enriched in sphingolipids (glucocerebrosides) and sterols (free sterols, acylated sterylglucosides and sterylglucosides).¹ Figure 1 shows the protein and lipid amounts in DRM during cold acclimation. DRM protein recovery rate from the plasma membrane was less than 10% and cold treatment resulted in a gradual decrease of the recovery: the recovery rate of DRM lipids from the plasma membrane rapidly decreased by half only after 2 days of cold acclimation. These data suggest a decrease in the proportion of microdomains in the plasma membrane and temporal changes in proteins and lipids in DRM during cold acclimation.Open in a separate windowFigure 1Changes in the protein and lipid amount in DRM recovered from plasma membrane fractions during cold acclimation. NA, non-acclimated; CA 2, CA 4 and CA 7, cold-acclimated for 2, 4 and 7 days, respectively. (Modified from Minami et al.)We found that there were significant differences in lipid alterations in plasma membrane and DRM fractions in cold acclimation (Fig. 2). The amount of total lipids (per mg of protein) in the plasma membrane fraction greatly increased after cold acclimation but not in the DRM fraction. In the plasma membrane fraction, cold acclimation for 2 days resulted in an increase in the proportions of phospholipids and free sterols and a decrease in the proportion of sphingolipids. In contrast, in the DRM fractions, free sterols increased after 2 days of cold acclimation but the proportion of phospholipids and sphingolipids did not change significantly. These results suggest that the changes in lipid classes in DRM differ from the changes in the whole plasma membrane. Our lipid analysis suggests that the decrease in sphingolipids in the plasma membrane affects the quantitative decrease of microdomains in the plasma membrane during cold acclimation (see Fig. 1). However, the lipid changes in the whole plasma membrane are unlikely to affect proportional changes in DRM-localized lipids except for free sterols.Open in a separate windowFigure 2Lipid changes in DRM and plasma membrane fractions during cold acclimation. NA, non-acclimated; CA 2, CA 4 and CA 7, cold-acclimated for 2, 4 and 7 days, respectively. FS, free sterols; ASG, acylated sterylglucosides; SG, sterylglucosides; GlcCer, glucocerebrosides; PL, phospholipids. (Modified from Minami et al.¹)We demonstrated quantitative changes of DRM-localized proteins during cold acclimation using two-dimensional differential gel electrophoresis (2D-DIGE) and western blot analyses.¹ 2D-DIGE analysis showed that one-third of the DRM-localized proteins quantitatively changed during cold acclimation. Subsequent mass spectrometric analysis of DRM proteins revealed significant changes in various proteins including increases in aquaporin, P-type H⁺-ATPase and endocytosis-related proteins and decreases in cytoskeletal proteins (tubulins and actins) and V-type H⁺-ATPase subunits during cold acclimation. The changes were first detected after 2 days of cold acclimation. Based on these results of protein analyses, Figure 3 illustrates changes in distribution patterns of DRM-localized proteins in the plasma membrane during cold acclimation. Cold acclimation induces the decrease in the amount of DRM proteins and lipids in the plasma membrane (Fig. 1), suggesting that component in microdomains decreases in the plasma membrane during cold acclimation. Furthermore, the proportion of some functional proteins changes in DRM during cold acclimation. Qualitative and quantitative changes of DRM proteins during cold acclimation are possibly associated with the plasma membrane functions. Plant cells at low temperature suffer from changes in membrane fluidity and cytoplasmic pH.^19–21 Upon freezing occurs, plant cells are subjected to severe dehydration and deformation stresses induced by extracellular ice formation.²² To avoid the occurrence of damages from these stresses, plants change plasma membrane components during cold acclimation.²³ H⁺-ATPase or aquaporins are thought to function in regulation of cytoplasmic pH or water transfer across the plasma membrane, respectively.^24,25 Cytoskeleton regulates cell structure and intracellular vesicle-trafficking processes reconstruct plasma membrane itself. Thus, the quantitative changes of these proteins in microdomains are likely associated with protective functions against freezing stress in cold acclimation.Open in a separate windowFigure 3Our hypothesis on changes in microdomains during plant cold acclimation. Cold acclimation results in a decrease in microdomains in the plasma membrane (see Fig. 1) and differential changes in various protein compositions in microdomains. We categorized DRM proteins as (1) membrane transport, (2) vesicle trafficking, (3) cytoskeleton, (4) microdomain-associated proteins and (5) others (e.g., plasma membrane and cell-wall reconstruction). Aquaporin, P-type H⁺-ATPase (1) and endocytosis-related proteins (2) increased and cytoskeletal proteins (3) and V-type H⁺-ATPase subunits (1) decreased in DRM during cold acclimation.We clearly demonstrated that cold acclimation decreased the amount of DRM and changed both lipid and protein compositions in plant DRM. Our study represents a first step towards elucidation of functions of plant microdomains in cold acclimation, strongly suggesting that microdomains, which function as a platform of membrane transport, membrane trafficking and cytoskeleton interaction, are associated with plant cold acclimation. Changes in microdomain lipids may also affect the protein activities during cold acclimation because sterols or sphingolipids are known to regulate activities of membrane transport or endocytosis. Thus, we suspect that the quantitative changes in microdomain lipids and proteins may correlate with development of freezing tolerance during cold acclimation. The hypothesis that the changes in microdomain components are functionally associated with plant cold acclimation should be reinforced by various approaches such as genetics, biochemistry or physical chemistry.