2D-DIGE analysis of mango (Mangifera indica L.) fruit reveals major proteomic changes associated with ripening

A comparative proteomic investigation between the pre-climacteric and climacteric mango fruits (cv. Keitt) was performed to identify protein species with variable abundance during ripening. Proteins were phenol-extracted from fruits, cyanine-dye-labeled, and separated on 2D gels at pH 4-7. Total spot count of about 373 proteins spots was detected in each gel and forty-seven were consistently different between pre-climacteric and climacteric fruits and were subjected to LC-MS/MS analysis. Functional classification revealed that protein species involved in carbon fixation and hormone biosynthesis decreased during ripening, whereas those related to catabolism and the stress-response, including oxidative stress and abiotic and pathogen defense factors, accumulated. In relation to fruit quality, protein species putatively involved in color development and pulp softening were also identified. This study on mango proteomics provides an overview of the biological processes that occur during ripening.     

Glycan Profiling of Plant Cell Wall Polymers using Microarrays

Plant cell walls are complex matrixes of heterogeneous glycans which play an important role in the physiology and development of plants and provide the raw materials for human societies (e.g. wood, paper, textile and biofuel industries)^1,2. However, understanding the biosynthesis and function of these components remains challenging.Cell wall glycans are chemically and conformationally diverse due to the complexity of their building blocks, the glycosyl residues. These form linkages at multiple positions and differ in ring structure, isomeric or anomeric configuration, and in addition, are substituted with an array of non-sugar residues. Glycan composition varies in different cell and/or tissue types or even sub-domains of a single cell wall³. Furthermore, their composition is also modified during development¹, or in response to environmental cues⁴.In excess of 2,000 genes have Plant cell walls are complex matrixes of heterogeneous glycans been predicted to be involved in cell wall glycan biosynthesis and modification in Arabidopsis⁵. However, relatively few of the biosynthetic genes have been functionally characterized ^4,5. Reverse genetics approaches are difficult because the genes are often differentially expressed, often at low levels, between cell types⁶. Also, mutant studies are often hindered by gene redundancy or compensatory mechanisms to ensure appropriate cell wall function is maintained⁷. Thus novel approaches are needed to rapidly characterise the diverse range of glycan structures and to facilitate functional genomics approaches to understanding cell wall biosynthesis and modification.Monoclonal antibodies (mAbs)^8,9 have emerged as an important tool for determining glycan structure and distribution in plants. These recognise distinct epitopes present within major classes of plant cell wall glycans, including pectins, xyloglucans, xylans, mannans, glucans and arabinogalactans. Recently their use has been extended to large-scale screening experiments to determine the relative abundance of glycans in a broad range of plant and tissue types simultaneously^9,10,11.Here we present a microarray-based glycan screening method called Comprehensive Microarray Polymer Profiling (CoMPP) (Figures 1 & 2)^10,11 that enables multiple samples (100 sec) to be screened using a miniaturised microarray platform with reduced reagent and sample volumes. The spot signals on the microarray can be formally quantified to give semi-quantitative data about glycan epitope occurrence. This approach is well suited to tracking glycan changes in complex biological systems¹² and providing a global overview of cell wall composition particularly when prior knowledge of this is unavailable.     

Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry

Label-based quantitative mass spectrometry analysis of affinity purified complexes, with its built-in negative controls and relative ease of use, is an increasingly popular choice for defining protein-protein interactions and multiprotein complexes. This approach, which differentially labels proteins/peptides from two or more populations and combines them prior to analysis, permits direct comparison of a protein pulldown (e.g. affinity purified tagged protein) to that of a control pulldown (e.g. affinity purified tag alone) in a single mass spectrometry (MS) run, thus avoiding the variability inherent in separate runs. The use of quantitative techniques has been driven in large part by significant improvements in the resolution and sensitivity of high-end mass spectrometers. Importantly, the availability of commercial reagents and open source identification/quantification software has made these powerful techniques accessible to nonspecialists. Benefits and drawbacks of the most popular labeling-based approaches are discussed here, and key steps/strategies for the use of labeling in quantitative immunoprecipitation experiments detailed.     

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.     

Using iRT, a normalized retention time for more targeted measurement of peptides

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.     

Analysis of the rat hypothalamus proteome by data‐independent label‐free LC‐MS/MS

Studies of neuronal, endocrine, and metabolic disorders would be facilitated by characterization of the hypothalamus proteome. Protein extracts prepared from 16 whole rat hypothalami were measured by data‐independent label‐free nano LC‐MS/MS. Peptide features were detected, aligned, and searched against a rat Swiss‐Prot database using ProteinLynx Global Server v.2.5. The final combined dataset comprised 21 455 peptides, corresponding to 622 unique proteins, each identified by a minimum of two distinct peptides. The majority of the proteins (69%) were cytosolic, and 16% were membrane proteins. Important proteins involved in neurological and synaptic function were identified including several members of the Ras‐related protein family and proteins involved in glutamate biosynthesis.     

利用免疫组织化学及蛋白质组学对树莓提取物抑制大鼠肝癌机制的研究

目的：探讨树莓预防大鼠原发性肝癌增殖抑制和凋亡诱导作用,寻找树莓预防大鼠原发性肝癌的特异性蛋白质靶点。方法：利用二乙基亚硝胺（DEN）建立大鼠原发性肝癌动物模型;通过免疫组织化学方法研究树莓提取物对于大鼠原发性肝癌的预防效果和形态学变化,利用蛋白质组学研究树莓预防大鼠原发性肝癌的特异性蛋白质靶点。结果：树莓提取物能抑制PCNAJVEGF的表达,抑制细胞增殖,并诱导细胞凋亡。蛋白质组学差异分析表明：成瘤组大鼠血清在蛋白质峰2597．93M／Z,4513．88M／Z上与高剂量树莓干预组大鼠血清具有显著性差异（P〈0．05）。结论：树莓提取物可以抑制肝癌细胞PCNA的表达,从而抑制肝癌细胞的增殖;还可以诱导肝癌细胞凋亡;蛋白质峰2597．93M／Z及4513．88M／Z所表达蛋白为其特异性作用靶点。     

ORP4L多克隆抗体的制备及其在蛋白质组学研究中的应用水

目的：原核表达并纯化人氧化固醇结合蛋白相关蛋白4（ORP4L）肽段,制备兔抗人ORP4L多克隆抗体,并利用其进行蛋白质组学研究。方法：应用PCR技术扩增人ORP4L382-485氨基酸（ORP4Lm）的基因序列并插入到PGEX-4T—1载体中,在大肠杆菌RosettaTM（DE3）中表达融合蛋白GST-ORP4Lm。利用所表达的融合蛋白中含有的GST标签进行亲和纯化。用所获得的纯化蛋白免疫新西兰大白兔,获得兔抗人ORP4L多克隆抗体。用Western blotting检测抗体免疫特异性。将亲和纯化后的抗体偶联到CNBr-actived sepharosC beads上,利用免疫沉淀的方法,通过质谱仪分析鉴定可能与ORP4L存在相互作用的蛋白质。通过West—ernblotting进一步确证特异性的相互作用蛋白。结果：在大肠杆菌中表达并纯化了GST-ORP4Lm重组蛋白,用其免疫新西兰大兔．成功制备了相应兔源多克隆抗体,Western blotting证实该抗体可以特异识别内源性及外源性的ORP4L蛋白。质谱分析和Western blotting的结果表明所制备的多克隆抗体可以用于蛋白质组学研究。结论：利用重组的GST-ORP4Lm融合蛋白成功制备了有良好特异性的ORP4L多克隆抗体,并可将其用于ORP4L的蛋白组学研究。     

Conjugated linoleic acid isomers modulate protein expression profile in rat hepatocytes

Conjugated linoleic acid (CLA) is a polyunsaturated fatty acid, which has been recently proven to be effective in reducing body fat mass, but brings as a side effect, the liver enlargement due to an increased lipid content. The in vivo lipogenic activity has been suggested to be due to the reduction in fat mass and to the consequent metabolism of blood glucose to fatty acid in the liver rather than in the adipose tissue. We investigated the ability of CLA to directly induce steatosis by modulating the expression pattern of hepatic proteins involved in lipid metabolism. To avoid interferences derived from CLA metabolism by other tissues, we used the in vitro model of freshly isolated rat hepatocytes incubated in the presence of different CLA isomers. The direct effect of CLA on lipid accumulation in hepatocytes was demonstrated by the altered expression pattern of several proteins involved in lipid metabolism, as assessed by two-dimensional gel electrophoresis and confirmed by Western blotting analysis. The CLA isomer c9,t11 was most effective in modulating the protein expression profile.     

蛋白质组学关键技术及其在茶树研究中的应用

蛋白质组学是后基因组时代的研究热点,相对于基因组学来说,能更直接、更准确的解释生命现象。对蛋白质组学关键技术如双向凝胶电泳、生物质谱、蛋白质芯片、生物信息学等及其在茶树上的应用作一介绍。