Effects of salinity levels on proteome of Suaeda aegyptiaca leaves

Saline soils are the major problem of cultivated lands of Iran. Suaeda aegyptiaca is a salt-tolerant plant (halophytes) that grow naturally in salt-affected areas of Iran. We have employed proteomics to identify the mechanisms of salt responsiveness in leaves of S. aegyptiaca grown under different salt concentrations. Ten-day-old plants were treated with 0, 150, 300, 450, and 600 mM NaCl. After 30 days of treatment, leaf samples were collected and analyzed using 2-D-PAGE. Out of 700 protein spots reproducible detected within replications, 102 spots showed significant response to salt treatment compared to 0 mM NaCl. We analyzed expression pattern of salt-responsive proteins using a hierarchical and two nonhierarchical (Fuzzy ART and SOM) statistical methods and concluded that Fuzzy ART is the superior method. Forty proteins of 12 different expression groups were analyzed using LC/MS/MS. Of these, 27 protein spots were identified including proteins involved in oxidative stress tolerance, glycinebetain synthesis, cytoskeleton remodeling, photosynthesis, ATP production, protein degradation, cyanide detoxification, and chaperone activities. The expression pattern of these proteins and their possible roles in the adaptation of S. aegyptiaca to salinity is discussed.     

Possible dysregulation of chaperon and metabolic proteins in cystic fibrosis bronchial tissue

Cystic fibrosis (CF) is an autosomal recessive disease due to mutations of the CF transmembrane conductance regulator gene. A systematic approach to generate a protein expressional pattern in CF bronchial tissue has not been performed so far. It was the aim of this hypothesis-generating study to construct differential proteomes of bronchial biopsies in controls (n = 8) and CF patients (n = 9). Biopsies (pools of three per patient) were taken; proteins were extracted and run on 2-DE with subsequent in-gel digestion and mass spectrometrical identification and quantification of proteins using specific software. Three hundred sixty-six protein spots were identified and compared between groups. Following an approach for multiple testing correction, the chaperone 75 kDa glucose-regulated protein and ubiquinol-cytochrome c reductase complex core protein I and one form of nidogen, a pseudogene of aconitase 2, were increased in CF (p < 0.005). Aberrant protein levels may reflect molecular changes of CF as well as CF-linked inflammation, infection and cellular stress response.     

Glutamine regulates the expression of proteins with a potential health-promoting effect in human intestinal Caco-2 cells

Glutamine is an essential amino acid for the enterocytes with respect to maintaining the gut mucosal integrity and function. This study was conducted to explore a molecular basis for the beneficial effects of glutamine on intestinal cells by searching for glutamine-dependent changes in the proteome. Caco-2 cells were exposed to different concentrations of L-glutamine with or without L-methionine sulfoximine, an inhibitor of the glutamine synthetase activity. 2-DE combined with MALDI-TOF-MS was used to identify proteins whose expression is changed by glutamine. To assess the relative protein synthesis rate, incorporation of L-[2H5]glutamine into individual proteins was monitored. The expression levels of 14 proteins changed significantly with the glutamine availability. Examples of differentially expressed proteins with potential health-promoting effects on the intestine are plasma retinol-binding protein, ornithine aminotransferase, apolipoprotein A-I, mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase, and acyl-CoA synthetase 5. Expression of these proteins was not changed by arginine deprivation. The differential change in the expression levels of the proteins was not correlated with their rate of synthesis, excluding an effect of glutamine depletion on general protein synthesis. Together, this study shows a gene-specific effect of glutamine on intestinal cells.     

Proteomic trajectory mapping of biological transformation: Application to developmental mouse retina

In this report we introduce a new concept "proteomic trajectory mapping" for the investigation of a complex phenomenon underlying biological transformation and transition. We define proteomic trajectory to be the kinetic trace of protein expression and present a successful proteomic trajectory mapping of complex molecular events underlying postnatal development of mouse retina. Cluster analysis of the trajectory data using a two-state model identified four proteomic trajectory types: two distinct trajectory types accounting for the decline or the rise of protein molecules actively expressed in the juvenile stage (J-type) or in the adult stage (A-type), a class of transient trajectories that mediate the transformation from the juvenile to the adult stage (T-type), and the steady trajectories throughout the entire process of transformation (C-type). The dominance of particular protein categories expressed in each trajectory characterizes the stage of retinal development. Proteomic trajectory mapping will be a powerful tool to study the systematic changes of protein expression caused by physiological, genetic, or pathological agents and the reverse of such changes to the norm by a treatment. The proteomic trajectory mapping is applicable to any biological transformation and, therefore, will be a powerful tool in biomedical sciences.     

Multivariate analysis of protein profiles of metal hyperaccumulator Thlaspi caerulescens accessions

Thlaspi caerulescens is increasingly acknowledged as one of the best models for studying metal hyperaccumulation in plants. In order to study the mechanisms underlying metal hyperaccumulation, we used proteomic profiling to identify differences in protein intensities among three T. caerulescens accessions with pronounced differences in tolerance, uptake and root to shoot translocation of Zn and Cd. Proteins were separated using two-dimensional electrophoresis and stained with SYPRO Orange. Intensity values and quality scores were obtained for each spot by using PDQuest software. Principal component analysis was used to test the separation of the protein profiles of the three plant accessions at various metal exposures, and to detect groups of proteins responsible for the differences. Spot sets representing individual proteins were analysed with the analysis of variance and non-parametric Kruskal-Wallis test. Clearest differences were seen among the Thlaspi accessions, while the effects of metal exposures were less pronounced. The 48 tentatively identified spots represent core metabolic functions (e.g. photosynthesis, nitrogen assimilation, carbohydrate metabolism) as well as putative signalling and regulatory functions. The possible roles of some of the proteins in heavy metal accumulation and tolerance are discussed.     

运用蛋白质组学技术研究与氨甲蝶呤耐药性相关的蛋白质

氨甲蝶呤（MTX）是一种重要的常用化疗药物,然而由于肿瘤细胞对其耐药性的增强而经常导致其疗效大大降低。为了寻找并鉴定与MTX耐药性相关的蛋白质从而为进一步闸明MTX的耐药机制提供线索,培养来源于小鼠NIH3T3的小鼠胚胎成纤维细胞系3T3R500与其耐300μmol／L MTX的细胞系MTX300,提取上述两种细胞系的总蛋白质,双向凝胶电泳分离蛋白质组成分,扫描并通过软件分析考马斯亮蓝染色的2-DE凝胶,选取表达差异最显著的点,胶内酶切后MALDI-TOF-MS进行肽指纹图谱（PMF）鉴定。图像分析显示,实验组和对照组的蛋白质组图谱之间,一些蛋白质点的表达有明显的变化。通过MALDI-TOF-MS和数据库查询,成功鉴定了耐药后表达变化最显著的蛋白质点为二氢叶酸还原酶（DHFR）,并通过Western blot验证了该结果,提示DHFR在MTX耐药机制中发挥重要作用。     

结核分枝杆菌菌体蛋白双向电泳技术的优化

目的：提取结核分枝杆菌菌体蛋白并建立一种利用双向电泳分离结核分枝杆菌蛋白质组的方法。方法：分离提取结核分枝杆菌菌体蛋白。样品采用不同pH梯度的鹏胶条进行第一向等电聚焦,12％SDS—PAGE凝胶进行二向电泳。银染后双向电泳图谱用Molecular Image Fx激光图像扫描仪扫描,PDQuest6．0软件完成配比分析。结果：优化了结核分枝杆菌菌体蛋白的提取方法,用裂解液8mol／L尿素结合2mol／L硫脲,140mmol／LDTT,0．5％biolyte,4％CHAPs,400mg／m1lOG处理,成功提取了蛋白,并通过结核分枝杆菌双向电泳技术体系的优化,建立了结核分枝杆菌菌体蛋白的分解图谱。pH4—7及pH7—10两胶面上共1387个点,占所检测到的蛋白总数的86％,绝大部分（1194个）蛋白位于pH4—7范围内。结论：为进一步开展结核分枝杆菌的比较蛋白质组学研究提供了方法学参考。     

An efficient strategy based on MAE, HPLC-DAD-ESI-MS/MS and 2D-prep-HPLC-DAD for the rapid extraction, separation, identification and purification of five active coumarin components from Radix Angelicae Dahuricae

Introduction – Further studies of active coumarin components in Radix Angelicae Dahuricae (AE) are absolutely essential to provide data on pharmacology, toxicology and quality for innovative drug candidates. Thus, the preparation of active component standards and the administration of coumarin monomers should be carried out. The isolation of the low‐level active components from complex Traditional Chinese Medicine (TCM) samples necessitates the development of rapid, simple and economical modern extraction, separation, identification and purification methods. Objective – To develop an efficient strategy for the rapid extraction, separation, identification and purification of coumarins from AE. Methodology – First, active coumarins in AE were extracted with microwave‐assisted extraction (MAE) after the extraction conditions were optimised. Second, gradient extraction methods with MAE were used to partially purify AE. Third, a high‐performance liquid chromatography–diode array detection‐electrospray ionisation tandem mass spectrometry (HPLC‐DAD‐ESI‐MS/MS) method was applied for the preliminary on‐line identification and screening of the main coumarins in AE extract. Finally, a two‐dimensional preparative high‐performance liquid chromatography–diode array detection (2D‐prep‐HPLC‐DAD) system was developed for further preparative separation of those target components. Results – Altogether 10 coumarins have been identified and five of them including xanthotoxol, osthenol, oxypeucedanin hydrate, byakangelicin and imperatorin were deemed as target components for the preparative isolation. All of the five isolated coumarins were at high purities of over 99% and the production rate was much higher than the traditional methods. Conclusion – The present paper demonstrates that these consecutive approaches are very useful for to isolate chemical constituents from TCM.     

Hide and seek: uncloaking the vegetative shoot apex of Arabidopsis thaliana

Leaf primordia are iteratively formed on the flanks of the shoot apical meristem (SAM) at the vegetative shoot apex of Arabidopsis thaliana. The youngest leaf primordia and the SAM are extensively covered by older proliferating leaves, making it difficult to obtain accurate volumetric data from these structures. Combination of serial histological sections combined with 3D reconstruction software allowed us to acquire such data. Here, we compared the SAMs of wild‐type plants of the Columbia‐0 and Landsberg erecta ecotypes with those of clavata3‐2 (clv3‐2) mutants, which produce an enlarged SAM. In addition, the SAM size and morphology of plants over‐expressing the gibberellin‐20 oxidase (GA20OX) gene was examined, and the effect of mild osmotic stress on primordium size was measured. Efficient 3D visualization of gene expression patterns is also possible with this method, as illustrated by the analysis of SHOOTMERISTEMLESS:GUS and WUSCHEL:GUS reporter lines.