An integrative proteome analysis of different seedling organs in tolerant and sensitive wheat cultivars under drought stress and recovery

Roots, leaves, and intermediate sections between roots and leaves (ISRL) of wheat seedlings show different physiological functions at the protein level. We performed the first integrative proteomic analysis of different tissues of the drought‐tolerant wheat cultivar Hanxuan 10 (HX‐10) and drought‐sensitive cultivar Chinese Spring (CS) during a simulated drought and recovery. Differentially expressed proteins (DEPs) in the roots (122), ISRLs (146), and leaves (163) showed significant changes in expression in response to drought stress and recovery. Numerous DEPs associated with cell defense and detoxifications were significantly regulated in roots and ISRLs, while in leaves, DEPs related to photosynthesis showed significant changes in expression. A significantly larger number of DEPs related to stress defense were upregulated in HX‐10 than in CS. Expression of six HSPs potentially related to drought tolerance was significantly upregulated under drought conditions, and these proteins were involved in a complex protein–protein interaction network. Further phosphorylation analysis showed that the phosphorylation levels of HSP60, HSP90, and HOP were upregulated in HX‐10 under drought stress. We present an overview of metabolic pathways in wheat seedlings based on abscisic acid signaling and important protein expression patterns.     

iTRAQ-Based Quantitative Proteomic Analysis of Cotton Roots and Leaves Reveals Pathways Associated with Salt Stress

Salinity is a major abiotic stress that affects plant growth and development. In this study, we performed a proteomic analysis of cotton roots and leaf tissue following exposure to saline stress. 611 and 1477 proteins were differentially expressed in the roots and leaves, respectively. In the roots, 259 (42%) proteins were up-regulated and 352 (58%) were down-regulated. In the leaves, 748 (51%) proteins were up-regulated and 729 (49%) were down-regulated. On the basis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we concluded that the phenylalanine metabolism and starch and sucrose metabolism were active for energy homeostasis to cope with salt stress in cotton roots. Moreover, photosynthesis, pyruvate metabolism, glycolysis / gluconeogenesis, carbon fixation in photosynthetic organisms and phenylalanine metabolism were inhabited to reduce energy consumption. Characterization of the signaling pathways will help elucidate the mechanism activated by cotton in response to salt stress.     

Comparative proteomic analysis of salt response proteins in seedling roots of two wheat varieties

A comparative proteomic analysis was made of salt response in seedling roots of wheat cultivars Jing-411 (salt tolerant) and Chinese Spring (salt sensitive) subjected to a range of salt stress concentrations (0.5%, 1.5% and 2.5%) for 2 days. One hundred and ninety eight differentially expressed protein spots (DEPs) were located with at least two-fold differences in abundance on 2-DE maps, of which 144 were identified by MALDI-TOF-TOF MS. These proteins were involved primarily in carbon metabolism (31.9%), detoxification and defense (12.5%), chaperones (5.6%) and signal transduction (4.9%). Comparative analysis showed that 41 DEPs were salt responsive with significant expression changes in both varieties under salt stress, and 99 (52 in Jing-411 and 47 in Chinese Spring) were variety specific. Only 15 and 9 DEPs in Jing-411 and Chinese Spring, respectively, were up-regulated in abundance under all three salt concentrations. All dynamics of the DEPs were analyzed across all treatments. Some salt responsive DEPs, such as guanine nucleotide-binding protein subunit beta-like protein, RuBisCO large subunit-binding protein subunit alpha and pathogenesis related protein 10, were up-regulated significantly in Jing-411 under all salt concentrations, whereas they were down-regulated in salinity-stressed Chinese Spring.     

杜仲叶片干旱胁迫响应相关差异蛋白的筛选与鉴定

为研究干旱胁迫下杜仲幼苗生理生化及分子响应机制,利用盆栽试验,通过持续（3、6、9、12、15 d）干旱胁迫处理和复水处理,研究杜仲幼苗的生理响应特性。同时,通过研究对照与处理15 d后的杜仲幼苗差异蛋白质组,分析杜仲幼苗对干旱胁迫的分子响应机制。结果表明,随着干旱处理时间的延长,杜仲叶片的水分饱和亏逐渐增加;光合速率、蒸腾速率、胞间二氧化碳浓度、气孔导度均逐渐减小;SOD、POD、CAT活性呈先上升后降低的趋势;丙二醛含量则呈现先上升,然后下降,最后又上升的变化特点;脯氨酸和可溶性糖含量的变化趋势与SOD等活性变化一致,前期上升,后期下降。在复水后,杜仲叶片的所有指标均有所恢复,但未达到干旱处理之前的水平。表明干旱胁迫影响了杜仲叶片的正常生长代谢。通过对干旱处理15 d后杜仲叶片总蛋白进行双向电泳分离和MALDI-TOF-TOF生物质谱鉴定,成功鉴定出36个差异表达蛋白,其中22个上调表达,14个下调表达。对36个差异蛋白进行功能分析发现,这些差异蛋白主要涉及信号传导、光合作用、碳代谢、能量代谢、次级代谢物合成、抗氧化保护酶、氨基酸代谢和蛋白质代谢。推测杜仲为适应干旱胁迫,首先是感应干旱胁迫信号,并传导至细胞内,影响杜仲叶片中光合作用、次级代谢物合成和蛋白质的生物合成;同时,通过过氧化物保护酶的作用,将过多活性氧加以清除;另一方面,则是通过增强糖酵解,磷酸戊糖途径,产生能量供杜仲正常生长所需。从生理机制来看,杜仲叶片同过增加胞内脯氨酸、可溶性糖含量,降低胞内渗透势,减少叶片中水分损失,与氨基酸合成和糖代谢相关蛋白的表达量上升的结果一致。     

青海高原春小麦PEG胁迫与复水后叶片差异蛋白质组学研究

春小麦是青海省的主要粮食作物,青海高原干旱频繁且严重,尤以春旱为首,对小麦生长发育造成严重影响．为了从蛋白质组学水平分析小麦对干旱胁迫的应答特征,探讨小麦可能的抗旱机制,本研究对青海主栽春小麦品种青春38幼苗进行聚乙二醇 (polyethylene glycol,PEG) 6000胁迫和复水处理,采用IEF/SDS PAGE双向凝胶电泳技术,对PEG胁迫和复水处理的小麦叶片总蛋白质分别与正常浇水的对照进行差异蛋白质组学研究,经考马斯亮蓝G 250染色获得清晰度和重复性较好的双向电泳图谱．PD Quest软件处理分析各对照和处理图谱,在等电点4.0～7.0线性范围内,均可识别650个以上清晰蛋白质点,获得比较明显的差异表达蛋白点43个,其中8个蛋白点重复.从35个差异蛋白点中选取24个差异点进行MALDI-TOF-TOF-MS肽质量指纹图谱分析,应用Mascot软件在NCBInr数据库中搜索鉴定蛋白质,得到22个阳性结果．对鉴定得到的差异表达蛋白进行功能分析,它们分别参与了光合作用、蛋白质合成、能量代谢途径、细胞防御、氧化还原、运输、信号转导等过程,而且根据差异表达蛋白功能分类所占比例,发现干旱胁迫与光合作用关系最为紧密.     

Proteomic analysis of Citrus sinensis roots and leaves in response to long-term magnesium-deficiency

Background

Magnesium (Mg)-deficiency is frequently observed in Citrus plantations and is responsible for the loss of productivity and poor fruit quality. Knowledge on the effects of Mg-deficiency on upstream targets is scarce. Seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were irrigated with Mg-deficient (0 mM MgSO₄) or Mg-sufficient (1 mM MgSO₄) nutrient solution for 16 weeks. Thereafter, we first investigated the proteomic responses of C. sinensis roots and leaves to Mg-deficiency using two-dimensional electrophoresis (2-DE) in order to (a) enrich our understanding of the molecular mechanisms of plants to deal with Mg-deficiency and (b) understand the molecular mechanisms by which Mg-deficiency lead to a decrease in photosynthesis.

Results

Fifty-nine upregulated and 31 downregulated protein spots were isolated in Mg-deficient leaves, while only 19 upregulated and 12 downregulated protein spots in Mg-deficient roots. Many Mg-deficiency-responsive proteins were involved in carbohydrate and energy metabolism, followed by protein metabolism, stress responses, nucleic acid metabolism, cell wall and cytoskeleton metabolism, lipid metabolism and cell transport. The larger changes in leaf proteome versus root one in response to Mg-deficiency was further supported by our observation that total soluble protein concentration was decreased by Mg-deficiency in leaves, but unaffected in roots. Mg-deficiency had decreased levels of proteins [i.e. ribulose-1,5-bisphosphate carboxylase (Rubisco), rubisco activase, oxygen evolving enhancer protein 1, photosynthetic electron transfer-like protein, ferredoxin-NADP reductase (FNR), aldolase] involved in photosynthesis, thus decreasing leaf photosynthesis. To cope with Mg-deficiency, C. sinensis leaves and roots might respond adaptively to Mg-deficiency through: improving leaf respiration and lowering root respiration, but increasing (decreasing) the levels of proteins related to ATP synthase in roots (leaves); enhancing the levels of proteins involved in reactive oxygen species (ROS) scavenging and other stress-responsive proteins; accelerating proteolytic cleavage of proteins by proteases, protein transport and amino acid metabolism; and upregulating the levels of proteins involved in cell wall and cytoskeleton metabolism.

Conclusions

Our results demonstrated that proteomics were more affected by long-term Mg-deficiency in leaves than in roots, and that the adaptive responses differed between roots and leaves when exposed to long-term Mg-deficiency. Mg-deficiency decreased the levels of many proteins involved in photosynthesis, thus decreasing leaf photosynthesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1462-z) contains supplementary material, which is available to authorized users.     

Photosynthesis-Related Proteins Play Crucial Role During Senescence Stage in Flue-Cured Tobacco Plants: A Combine iTRAQ-PRM Study

Leaf aging is a significant process during herbaceous plant senescence, which is influenced by various internal and external factors. During leaf aging, chlorophyll catabolism is one of the most important metabolism pathways and results in leaf yellowing. Understanding the underlying mechanism is important for the regulation of senescence in tobacco leaf. However, there are few studies on explaining tobacco leaf senescence from the proteomics level. Here, photosynthesis experiments, cell ultrastructure, and proteomics were used to study tobacco leaves of different growth stages. We applied iTRAQ-based quantitative proteomics and parallel reaction monitoring (PRM) to determine the accumulation of proteins in aging tobacco leaves. Overall, we screened 4747 proteins. The result of KEGG pathways analysis showed that differently expressed proteins (DEPs) were involved in four pathways: metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and starch and sucrose metabolism. This would be first report based on iTRAQ-PRM technique, in which we identified proteins related to photosynthesis showed a differently expressed during senescence stage in flue-cured tobacco plants.

     

Intrinsic morphology and spatial distribution of non-structural carbohydrates contribute to drought resistance of two mulberry cultivars

• Drought is one of the most adverse environmental stresses limiting plant growth and productivity. However, the underlying mechanisms regarding metabolism of non-structural carbohydrates (NSC) in source and sink organs are still not fully elucidated in woody trees.
• Saplings of mulberry cv Zhongshen1 and Wubu were subjected to a 15-day progressive drought stress. NSC levels and gene expression involved in NSC metabolism were investigated in roots and leaves. Growth performance and photosynthesis, leaf stomatal morphology, and other physiological parameters were also analysed.
• Under well-watered conditions, Wubu had a higher R/S, with higher NSC in leaves than in roots; Zhongshen1 had a lower R/S with higher NSC in roots than leaves. Under drought stress, Zhongshen1 showed decreased productivity and increased proline, abscisic acid, ROS content and activity of antioxidant enzymes, while Wubu sustained comparable productivity and photosynthesis. Interestingly, drought resulted in decreased starch and slightly increased soluble sugars in leaves of Wubu, accompanied by notable downregulation of starch-synthesizing genes and upregulation of starch-degrading genes. Similar patterns in NSC levels and relevant gene expression were also observed in roots of Zhongshen1. Concurrently, soluble sugars decreased and starch was unchanged in roots of Wubu and leaves of Zhongshen1. However, gene expression of starch metabolism in roots of Wubu was unaltered, but in leaves of Zhongshen1 starch metabolism was more activated.
• These findings revealed that intrinsic R/S and spatial distribution of NSC in roots and leaves concomitantly contribute to drought resistance in mulberry.

     

Quantitative Proteomics Analysis Identifies the Potential Mechanism Underlying Yellow-Green Leave Mutant in Wheat

Enhancing photosynthesis efficiency is considered as one of the most crucial targets during wheat breeding. However, the molecular basis underlying high photosynthesis efficiency is not well understood up to now. In this study, we investigated the protein expression profile of wheat Jimai5265yg mutant, which is a yellow-green mutant with chlorophylls b deficiency but high photosynthesis efficiency. Though TMT-labeling quantitative proteomics analysis, a total of 72 differential expressed proteins (DEPs) were obtained between the mutant and wild type (WT). GO analysis found that they significantly enriched in thylakoid membrane, pigment binding, magnesium chelatase activity and response to light intensity. KEGG analysis showed that they involved in photosynthesis-antenna protein as well as porphyrin and chlorophyll metabolism. Finally, 118 RNA editing events were found between mutant and WT genotype. The A to C editing in the 3-UTR of TraesCS6D02G401500 lead to its high expression in mutant through removing the inhibition of tae-miR9781, which might have vital role in regulating the yellow-green mutant. This study provided some useful clues about the molecular basis of Jimai5265yg mutant as well as chlorophylls metabolism in wheat.     

Identification of changes in Triticum aestivum L. leaf proteome in response to drought stress by 2D-PAGE and MALDI-TOF/TOF mass spectrometry

Drought is an abiotic stress that strongly influences plant growth, development and productivity. To gain a better understanding of the drought-stress responses at physiological and molecular level in wheat plants (Triticum aestivum cv. KTC86211), we performed a comparative physiological and proteomics analysis. Eight-day-old wheat seedlings were treated with polyethylene glycol-simulated drought stress for 0, 24, 48 and 72 h. Drought treatment resulted in alterations of morphology, increased relative electrolyte leakage and reduced length and weight on leaf and root. Stress-induced proteome changes were analyzed by two-dimensional gel electrophoresis in conjunction with MALDI-TOF/TOF. Twenty-three spots differed significantly between control and treated plants following 48 h of drought stress, with 19 upregulated, and 4 downregulated, in leaf tissues. All of the differentially expressed protein spots were identified, revealing that the majority of proteins altered by drought treatment were involved in reactive oxygen species scavenging enzymes and photosynthesis. Other proteins identified were involved in protein metabolism, cytoskeleton structure, defense response, acid metabolism and signal transduction. All proteins might contribute cooperatively to reestablish cellular homeostasis under drought stress. The present study not only provides new insights into the mechanisms of acclimation and tolerance to drought stress in wheat plants, but also provides clues for improving wheat’s drought tolerance through breeding or genetic engineering.     

Differential proteomic analysis of polyubiquitin-related proteins in chemical hybridization agent-induced wheat (Triticum aestivum L.) male sterility

Protein polyubiquitination is a significant regulator of diverse physiological functions, including sexual reproduction, in plants. Chemical hybridizing agents (CHA) SQ-1 has been shown to induce male sterility in wheat (Triticum aestivum L.) through inhibition of pollen development. This mechanism by which CHA induces male sterility in wheat is unclear. In this study, differential proteomic analysis of polyubiquitinated proteins associated with wheat male sterility was investigated. Wheat plants of the same genetic background were treated with or without CHA. Ubiquitinated proteins were then extracted and enriched for proteomic analysis. Differentially expressed polyubiquitinated proteins in trinuclear stage anther were identified by nanospray liquid chromatography/tandem mass spectrometry. A total of 127 and 131 differentially expressed polyubiquitinated proteins, including heat shock protein 70, ATPase subunit, glycosyltransferase, ubiquitin-related enzyme, and 20S proteasome subunit, were successfully identified by searching against wheat protein database and NCBInr database, respectively. Most of these proteins are related to photosynthesis, carbohydrate and energy metabolism, and multiple metabolic processes. These findings show that alteration of polyubiquitinated proteins is associated with male sterility in wheat.