A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis

Four fractions from rat liver (a crude mitochondria (CM) and cytosol (C) fraction obtained with differential centrifugation, a purified mitochondrial (PM) fraction obtained with nycodenz density gradient centrifugation, and a total liver (TL) fraction) were analyzed with two-dimensional liquid chromatography tandem mass spectrometry analysis. A total of 564 rat proteins were identified and were bioinformatically annotated according to their physicochemical characteristics and functions. While most extreme alkaline ribosomal proteins were identified in the TL fraction, the C fraction mainly included neutral enzymes and the PM fraction enriched alkaline proteins and proteins with electron transfer activity or oxygen binding activity. Such characteristics were more apparent in proteins identified only in the TL, C, or PM fraction. The Swiss-Prot annotation and the bioinformatic prediction results proved that the C and PM fractions had enriched cytoplasmic or mitochondrial proteins, respectively. Combination usage of subcellular fractionation with two-dimensional liquid chromatography tandem mass spectrometry was proved to be a high-throughput, sensitive, and effective analytical approach for subcellular proteomics research. Using such a strategy, we have constructed the largest proteome database to date for rat liver (564 rat proteins) and its cytosol (222 rat proteins) and mitochondrial fractions (227 rat proteins). Moreover, the 352 proteins with Swiss-Prot subcellular location annotation in the 564 identified proteins were used as an actual subcellular proteome dataset to evaluate the widely used bioinformatics tools such as PSORT, TargetP, TMHMM, and GRAVY.     

Quantitative analysis of severe acute respiratory syndrome (SARS)-associated coronavirus-infected cells using proteomic approaches: implications for cellular responses to virus infection

We present the first proteomic analysis on the cellular response to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection. The differential proteomes of Vero E6 cells with and without infection of the SARS-CoV were resolved and quantitated with two-dimensional differential gel electrophoresis followed by ESI-MS/MS identification. Moreover isotope-coded affinity tag technology coupled with two-dimensional LC-MS/MS were also applied to the differential proteins of infected cells. By combining these two complementary strategies, 355 unique proteins were identified and quantitated with 186 of them differentially expressed (at least 1.5-fold quantitative alteration) between infected and uninfected Vero E6 cells. The implication for cellular responses to virus infection was analyzed in depth according to the proteomic results. Thus, the present work provides large scale protein-related information to investigate the mechanism of SARS-CoV infection and pathogenesis.     

Proteomic analysis of hepatitis B virus-associated hepatocellular carcinoma: Identification of potential tumor markers

Hepatocellular carcinoma (HCC) is a malignancy of both underdeveloped and developing countries. Proteomes of ten pairs of clinical hepatitis B virus associated HCC tissue samples were obtained by high resolution two-dimensional gel electrophoresis. Comprehensive analyses of proteins associated with B-type HCC were focused on total differentially expressed proteins (> or = two-fold increase or decrease, Student's t-test, p < 0.05) from one pair of samples. Protein identification was done by peptide mass fingerprinting with matrix assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Comparative analyses of proteins associated with B-type HCC included repeat statistics in ten cases. A total of 100 protein spots, corresponding to 80 different gene products, were identified. Proteins whose expression levels were different by more than 2-fold in at least 50% of the cases (five of ten cases) were further analyzed and 45 proteins were selected out as candidates for HCC-associated proteins. Western blotting further validated up-regulated expressions of two candidate proteins in tumor tissues: proliferating cell antigen and stathmin 1. This comprehensive and comparative analyses of proteins associated with B-type HCC could provide useful molecular markers for diagnostics and prognostics and for therapeutic targets. The physiological significance of the differential expressions for several candidate proteins are discussed.     

毛细管电泳飞摩尔水平分析糖蛋白中唾液酸

利用毛细管电泳分析唾液酸2-氨基吖啶酮(AMAC)衍生物方法, 可在飞摩尔水平分析糖蛋白中唾液酸. 重组人促红细胞生成素(rhu-EPO)、人尿胰蛋白酶抑制剂(hu-UTI)中唾液酸分析结果与文献值符合较好; 而牛α₁-酸性糖蛋白(α₁-AGP)分析结果与早期文献值相比, 存在一定差异, 并发现该糖蛋白中除含有5-N-乙酰氨基唾液酸(Neu5Ac)外, 还含数量与Neu5Ac相当的5-N-乙醇酰氨基唾液酸(Neu5Gc).     

人类新型β 3半乳糖基转移酶基因β 3GalT7 的克隆和鉴定

从人肺 cDNA 文库中克隆到人类β 3- 半乳糖基转移酶家族中的一个新成员β 3GalT7 (AY277592 , EC2.4.1.-) ,并对其进行了鉴定 . 该基因定位在人类染色体 19q13.2. 它包含一个 1 191 bp 的开放阅读框 (ORF). 编码的蛋白质包括一个信号肽和一个半乳糖基转移酶结构域,分子质量和等电点分别为 43.3 ku 和 8.37. 从原核表达中获得的融合蛋白的分子质量和预测相符 . RNA 印迹杂交显示β 3GalT7 在肺、喉和回肠组织中高表达,而在舌、乳房、子宫、睾丸等组织中表达较低 . 此外半定量 RT-PCR 显示β 3GalT7 在人类不同的肿瘤细胞中转录水平有明显差异 .     

表位标签技术在膜蛋白研究中的应用

膜蛋白的研究包括埘膜蛋白在细胞内的运输和定位,膜蛋白的结构和功能,以及膜蛋白和其他蛋白质间的相互作用等方面的研究.在研究过程中,如果能够基于膜蛋白的拓扑学结构预测,选择合适的表位标签,利用基因融合技术在基因水平上对膜蛋白进行改造,可以产生含有表位标签的重组膜蛋白,不仅具有原有膜蛋白的功能活性,还能够被抗体特异性识别,并且结合相关的免疫荧光检测技术,将会极大地促进膜蛋白的结构和功能研究.本文就目前膜蛋白研究中所涉及的表位标签技术及其应用策略和所取得的进展作一简述.     

小鼠cAMP依赖的蛋白激酶催化亚基α的重组表达研究

将小鼠ｃＡＭＰ依赖的蛋白激酶（ｃＡＰＫ）催化亚基α（ｍＣα）分别以成熟、麦芽糖结合蛋白（ＭＢＰ）融合以及Ｎ端连续六个组氨酸（Ｈｉｓ_６）融合的形式在大肠杆菌中得到了高效表达,且成熟及融合的重组ｍＣα均有明显的蛋白激酶活性,表明蛋白激酶催化核心结构具有相对的独立性。其中Ｈｉｓ_６－ｍＣα可利用金属离子（Ｎｉ￣（２＋））配体亲和层析（Ⅰ－ＭＡＣ）一步纯化,所得融合蛋白可通过Ｈｉｓ_６亲合手臂（Ｔａｇ）固相化于金属离子（Ｎｉ￣（２＋））配体亲和树脂上,为进一步利用ＰｈａｇｅＤｉｓｐｌａｙ多肽库筛选ｃＡＰＫ识别的底物序列和专一性抑制剂打下了基础。     

Fibronectin and Focal Adhesion Kinase Small Interfering RNA Modulate Rat Retinal Müller Cells Adhesion and Migration

Retinal Müller cells (RMCs) hypertrophy and proliferation play a crucial role in epiretinal membrane formation. This study was designed to analyze the effects of Fibronectin and specific FAK siRNA in cell adhesion and migration in rat Müller cells. RMCs were cultured and identified by GFAP, Vimentin, and GLAST mAb, respectively. The cells were planted on dishes coated with Fibronectin at 0, 1, 5, 10, 50, and 100 μg/ml. The attachment and migration assay was applied to characterize the RMCs–Fibronectin interactions. Cell lysis and Western blotting were utilized to detect β₁-integrin, FAK, and GLAST protein expression. Then the cells were treated with FAK siRNA, non-targeting siRNA, and control medium. The cell cycle and apoptosis rate was determined by flow cytometry. The attachment, migration, and Western blotting assay were repeated. These data suggested that almost all the cells expressed GFAP, Vimentin, and GLAST, respectively, which ensured most of the harvested cells were RMCs. In attachment assay, the A570 values increased significantly with time (F = 1105.439, P < 0.001) and Fibronectin concentration (F = 424.683, P < 0.001). There were significant difference between each Fibronectin concentration in RMCs migration (F = 34.703, P < 0.000). The expression ratio of FAK, β₁-integrin, and GLAST elevated significantly as Fibronectin concentration increased (F = 54.755, P < 0.000; F = 119.962, P < 0.000; F = 39.287, P < 0.000). The Fibronectin pretreatment was settled on 50 μg/ml for siRNA inhibition assays. The specific FAK siRNA treatment significantly increased G₀/G₁ percentage and apoptosis rate compared with NT siRNA and control group (F = 11.526, P = 0.009; F = 64.772, P < 0.000). The apoptotic rate was significantly suppressed by inhibitors of caspase-8 and 3 (F = 10.500, P = 0.011). The A570 values were significantly suppressed in FAK siRNA groups compared with NT siRNA and control group (F = 154.241, P < 0.000), and the mean migratory cells per view field were significantly decreased (F = 10.906, P = 0.001). FAK and GLAST expression ratio decreased significantly after FAK siRNA treatment (F = 5.315, P = 0.047; F = 5.985, P = 0.042). Take together, FAK is involved in β₁-integrin mediated adhesive signaling and play a critical role in regulating Müller cell adhesion, migration, and so far as to glutamate transportation functions.     

Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification

A resurgence of interest in the human plasma proteome has occurred in recent years because it holds great promise of revolution in disease diagnosis and therapeutic monitoring. As one of the most powerful separation techniques, multidimensional liquid chromatography has attracted extensive attention, but most published works have focused on the fractionation of tryptic peptides. In this study, proteins from human plasma were prefractionated by online sequential strong cation exchange chromatography and reversed-phase chromatography. The resulting 30 samples were individually digested by trypsin, and analyzed by capillary reversed-phase liquid chromatography coupled with linear ion trap mass spectrometry. After meeting stringent criteria, a total of 1292 distinct proteins were successfully identified in our work, among which, some proteins known to be present in serum in <10 ng/mL were detected. Compared with other works in published literatures, this analysis offered a more full-scale list of the plasma proteome. Considering our strategy allows high throughput of protein identification in serum, the prefractionation of proteins before MS analysis is a simple and effective method to facilitate human plasma proteome research.     

Effect of Continuous Positive Airway Pressure on Adiponectin in Patients with Obstructive Sleep Apnea: A Meta-Analysis

Objective

Obstructive sleep apnea (OSA) has been suggested to be associated with low levels of adiponectin. Continuous positive airway pressure (CPAP) is the gold standard treatment for OSA; however, previous studies assessing the effect of CPAP on adiponectin in patients with OSA yielded conflicting results. The present meta-analysis was performed to determine whether CPAP therapy could increase adiponectin levels.

Methods

Two reviewers independently searched PubMed, Cochrane library, Embase and Web of Science before February 2015. Information on characteristics of subjects, study design and pre- and post-CPAP treatment of serum adiponectin was extracted for analysis. Standardized mean difference (SMD) was used to analyze the summary estimates for CPAP therapy.

Results

Eleven studies involving 240 patients were included in this meta-analysis, including ten observational studies and one randomized controlled study. The meta-analysis showed that there was no change of adiponectin levels before and after CPAP treatment in OSA patients (SMD = 0.059, 95% confidence interval (CI) = −0.250 to 0.368, z = 0.37, p = 0.710). Subgroup analyses indicated that the results were not affected by age, baseline body mass index, severity of OSA, CPAP therapy duration, sample size and racial differences.

Conclusions

This meta-analysis suggested that CPAP therapy has no impact on adiponectin in OSA patients, without significant changes in body weight. Further large-scale, well-designed long-term interventional investigations are needed to clarify this issue.