植物细胞壁蛋白质组学研究进展

植物细胞壁蛋白质在细胞代谢和发育调控、细胞壁组分修饰、信号转导及胁迫响应等生物学事件中具有重要功能.最近,国内外学者开展了大量植物细胞壁蛋白质组学的研究工作,并取得了巨大进展.本文详述了细胞壁蛋白质的分类、提取、鉴定及生物信息学分析的最新进展,总结了植物细胞壁蛋白质组学的应用和面临的挑战,提出了植物细胞壁蛋白质组学研究的框架图,以期为植物细胞壁蛋白质组学的广泛研究提供借鉴.     

蛋白质组学研究技术及其在寄生虫学中的应用

介绍了蛋白质组学研究的核心技术 ,即蛋白质组分分离、蛋白质组分鉴定、利用蛋白质组信息学进行结构和功能预测 ,以及蛋白质组学技术在寄生虫学中的应用和研究进展。     

蛋白质组学中新蛋白质鉴定的研究方法和策略

当前,基于生物质谱进行蛋白质鉴定的技术已经成为蛋白质组学研究的支撑技术之一.产生的数据主要使用数据库搜索的方法进行处理,这种方法的一大缺陷是不能鉴定数据库中未包含的蛋白质,因此如何充分利用质谱数据对蛋白质组研究的意义很大,而新蛋白质鉴定更是其中一个重要的内容.新蛋白质鉴定是蛋白质鉴定的一个方面,新蛋白质的定义按照序列和功能的已知程度分为3个层次;以蛋白质鉴定的方法为基础,目前新蛋白质鉴定的方法可分为denovo测序和相似序列搜索结合的方法以及搜索EST、基因组等核酸数据库的方法2大类;两者各有利弊.存在各自的问题和相应处理的策略.不同的研究者可以根据具体目的应用和发展不同的鉴定方法,同时新蛋白质的鉴定也将随着蛋白质组学研究的发展而更加完善.     

蛋白质组学在感染性疾病研究中的应用

蛋白质组学在人类疾病研究中的应用 ,主要是通过比较分析正常组织细胞与异常组织细胞、同一疾病在不同的发展时期细胞内整体蛋白质的表达差异 ,对差异表达的蛋白质进行鉴定、定量、表征 ,寻找与疾病相关的新的标志物 ,为人类疾病研究提供新的手段和依据 ,蛋白质组学在感染性疾病研究中的应用就是其中的一个方面。1 .蛋白质组学在感染性疾病研究中的应用蛋白质组学在人类感染性疾病研究中的应用主要是对引起感染性疾病的致病源的整体蛋白质进行研究 ,同时结合血清学 ,对其进行分析 ,鉴定出与疾病相关的新的标志物 ,为感染性疾病的诊断、治疗…     

植物蛋白质组学研究若干重要进展

植物蛋白质组学近年来正从定性向精确定量蛋白质组学的方向发展。国际上近两年发表的约160篇研究论文报道了利用不断改进的双向电泳结合生物质谱技术、多维蛋白质鉴定技术, 以及包括双向荧光差异凝胶电泳、15N体内代谢标记、同位素标记的亲和标签、同位素标记相对和绝对定量等在内的第2代蛋白质组学技术, 对植物组织(器官)与细胞器、植物发育过程和植物响应环境胁迫的蛋白质组特征, 以及植物蛋白质翻译后修饰和蛋白质相互作用等方面的研究成果。该文对上述报道进行总结, 综述了2007年以来植物蛋白质组学若干重要问题研究的新进展。     

基于电子捕获裂解/电子转运裂解串联质谱技术的蛋白质组学研究

蛋白质组学的兴起带动了质谱技术的快速发展,而质谱技术的进步则拓宽了蛋白质组学研究问题的广度.最近10年内,肽段或完整蛋白质在质谱仪中的裂解技术——电子捕获裂解(electron capture dissociation,ECD)与电子转运裂解(electron transfer dissociation,ETD)逐渐发展起来.ECD和ETD在蛋白质组学中的应用,特别是在蛋白质的翻译后修饰鉴定和自顶而下(Top-down)的完整蛋白质裂解研究中已经展示出了诱人的前景.对ECD和ETD的基本原理、质谱特点、仪器实现、数据解析算法与软件开发,以及在蛋白质组学中的应用进展等方面进行了比较系统全面的阐述,并对当前的研究问题、面临的技术挑战与未来的发展趋势等方面作了深入剖析.     

定量蛋白质组同位素标记技术及应用

定量蛋白质组学是对蛋白质组进行精确的定量和鉴定的学科,突破了传统蛋白质组研究集中于对蛋白质的分离和鉴定,着重于定性定量解析细胞蛋白质的动态变化信息,更真实地反映了细胞功能、过程机制等综合信息。以同位素为内标的质谱分析新技术的提出,显示出可同时自动鉴定和精确定量的能力,代表了目前定量蛋白质组研究的主要发展方向。对近年来定量蛋白质组学同位素标记技术和应用研究所取得的重要进展以及最新的发展动态进行了综述。     

蛋白质组学在研究植物响应逆境机理上的应用

逆境条件下植物可以通过改变其基因表达和相关代谢活动来适应,探讨植物基因和蛋白表达谱的变化就成为植物逆境响应机制研究中的重要内容,蛋白质表达谱反映了植物细胞和组织的实际状态,是植物基因表达和最终代谢的关键环节。随着蛋白质分离技术、质谱鉴定技术和植物生物信息学的迅速发展,蛋白质组学在植物响应逆境方面的研究中的应用已经比较成功,加深了人们对植物响应逆境机制的认识,并为人们提供了新的线索和思维。本文主要对蛋白质组学在植物响应非生物逆境(干旱、盐胁迫、低温胁迫、高温胁迫等)和生物逆境(病虫害)的机制研究的应用上进行了综述。     

中国蛋白质组学研究进展——以人类肝脏蛋白质组计划和蛋白质组学技术发展为主题

蛋白质组学是对细胞或生物体全部蛋白质的系统鉴定、定量并阐释其生物学功能的学科.自21世纪初期开始,随着高精度、高灵敏度和快速扫描质谱仪的出现和快速发展以及微量蛋白质组样品高效分离技术的进步,蛋白质组学获得了快速发展,并在生理过程与病理机制研究等几乎所有生命科学研究领域得到了广泛的应用.过去10年,中国蛋白质组学研究在政府的支持和广大蛋白质组学研究人员的努力下呈现出腾飞式的发展态势.本文综述了人类肝脏蛋白质组计划和2010~2013年中国蛋白质组学技术的发展.     

蛋白质组学技术及其在糖尿病研究中的应用

蛋白质组学是以基因编码蛋白质作为研究对象,并依赖高通量、高自动化的技术对其进行大规模分析的一门学科.其研究方法及手段,已用于糖尿病研究领域.对蛋白质组样品提取技术、蛋白质组分离和分析技术(双向电泳、色谱、质谱分析)、生物信息学以及蛋白质组学技术在研究1型糖尿病(T1DM)、2型糖尿病(T2DM)、胰岛素抵抗等的发病机制以及抗糖尿病药物的开发中的应用等进行了综述.     

Thematic Review Series: Proteomics: Lipoproteomics: using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins

Lipoproteins are centrally important in lipid transport, fuel metabolism, and cardiovascular disease. The prototypic lipoprotein has an outer shell of amphipathic lipids and proteins that solubilizes a hydrophobic lipid core. Lipoprotein-associated proteins have classically been viewed as structural elements and factors important in lipid metabolism. Recent mass spectrometric analyses reveal that the protein cargo of lipoproteins is much more diverse than previously appreciated, raising the possibility that lipoproteins play previously unsuspected roles in host defense mechanisms and inflammation. They further suggest that lipoprotein-associated proteins can identify humans at increased risk of cardiovascular disease. Here, we summarize recent developments in lipoproteomics, the proteomic analysis of lipoproteins. We also discuss the promises and challenges this powerful analytical strategy offers for expanding our understanding of the biology and structures of lipoproteins.     

Plasma lipoproteome in Alzheimer’s disease: a proof-of-concept study

Background

Although total plasma lipoproteome consists of proteins that have shown promises as biomarkers that can identify Alzheimer’s disease (AD), effect sizes are modest. The objective of this study is to provide initial proof-of-concept that the plasma lipoproteome more likely differ between AD cases and controls when measured in individual plasma lipoprotein fractions than when measured as total in immunodepleted plasma.

Methods

We first developed a targeted proteomics method based on selected reaction monitoring (SRM) and liquid chromatography and tandem mass spectrometry for measurement of 120 tryptic peptides from 79 proteins that are commonly present in plasma lipoproteins. Then in a proof-of concept case–control study of 5 AD cases and 5 sex- and age-matched controls, we applied the targeted proteomic method and performed relatively quantification of 120 tryptic peptides in plasma lipoprotein fractions (fractionated by sequential gradient ultracentrifugation) and in immunodepleted plasma (of albumin and IgG). Unadjusted p values from two-sample t-tests and overall fold change was used to evaluate a peptide relative difference between AD cases and controls, with lower p values (<?0.05) or greater fold differences (>?1.05 or?<?0.95) suggestive of greater peptide/protein differences.

Results

Within-day and between-days technical precisions (mean %CV [SD] of all SRM transitions) of the targeted proteomic method were 3.95% (2.65) and 9.31% (5.59), respectively. Between-days technical precisions (mean % CV [SD]) of the entire plasma lipoproteomic workflow including plasma lipoprotein fractionation was 27.90% (14.61). Ten tryptic peptides that belonged to 5 proteins in plasma lipoproteins had unadjusted p values?<?0.05, compared to no peptides in immunodepleted plasma. Furthermore, 27, 32, 17, and 20 tryptic peptides in VLDL, IDL, LDL and HDL, demonstrated overall peptide fold differences?>?1.05 or?<?0.95, compared to only 6 tryptic peptides in immunodepleted plasma. The overall comparisons, therefore, suggested greater peptide/protein differences in plasma lipoproteome when measured in individual plasma lipoproteins than as total in immunodepleted plasma. Specifically, protein complement C3’s peptide IHWESASLLR, had unadjusted p values of 0.00007, 0.00012, and 0.0006 and overall 1.25, 1.17, 1.14-fold changes in VLDL, IDL, and LDL, respectively. After positive False Discovery Rate (pFDR) adjustment, the complement C3 peptide IHWESASLLR in VLDL remained statistically different (adjusted p value?<?0.05).

Discussion

The findings may warrant future studies to investigate plasma lipoproteome when measured in individual plasma lipoprotein fractions for AD diagnosis.

     

Synthesis and release of low density lipoproteins by the isolated perfused pig liver.

In previous studies, we have shown that a relatively large amount of low density lipoproteins is released into the perfusate during isolated pig liver perfusion. The present studies were done to determine the source of these lipoproteins. Breakdown of the very low density lipoproteins to low density lipoproteins by the perfusion apparatus or by hepatic catabolism was excluded by adding 125I very low density lipoproteins to the perfusate in the presence and absence of a liver and then measuring the radioactivity in the low density lipoprotein fraction after rate-zonal ultracentrifugation. Release of preformed low density, lipoproteins from the liver was investigated by injecting iodine-labeled low density lipoproteins in vivo several hours prior to perfusion of the liver and then measuring the release of labeled low density lipoproteins into the perfusate. It was shown that intact labeled low density lipoproteins were released by the perfused liver. De novo synthesis of the low density lipoproteins was established by measuring the incorporation of [1-14C]leucine into this lipoprotein fraction. The radioactivity in the low density lipoprotein fraction increased with time and accounted for 20 to 25% of the total radioactivity incorporated into all the lipoprotein fractions. The incorporation of [1-14C]leucine into the low density lipoproteins was confirmed by rate-zonal analysis. We conclude that the low density lipoproteins in the perfusate from pig liver perfusions were derived mainly from a preformed liver pool, but also partly from de novo synthesis by the liver.     

Rapid method for the isolation of lipoproteins from human serum by precipitation with polyanions

Procedures are described for the isolation of lipoproteins from human serum by precipitation with polyanions and divalent cations. A mixture of low and very low density lipoproteins can be prepared without ultracentrifugation by precipitation with heparin and either MnCl(2) alone or MgCl(2) plus sucrose. In both cases the precipitation is reversible, selective, and complete. The highly concentrated isolated lipoproteins are free of other plasma proteins as judged by immunological and electrophoretic methods. The low density and very low density lipoproteins can then be separated from each other by ultracentrifugation. The advantage of the method is that large amounts of lipoproteins can be prepared with only a single preparative ultracentrifugation. Polyanions other than heparin may also be used; when the precipitation of the low and very low density lipoproteins is achieved with dextran sulfate and MnCl(2), or sodium phosphotungstate and MgCl(2), the high density lipoproteins can subsequently be precipitated by increasing the concentrations of the reagents. These lipoproteins, containing small amounts of protein contaminants, are further purified by ultracentrifugation at d 1.22. With a single preparative ultracentrifugation, immunologically pure high density lipoproteins can be isolated from large volumes of serum.     

Apolipoprotein specificity of the chicken oocyte receptor for low and very low density lipoproteins: lack of recognition of apolipoprotein VLDL-II

At onset of egg-laying in the chicken, plasma levels of apolipoprotein VLDL-II (apoII) increase dramatically, suggesting a function of apoII in yolk deposition of triglyceride-rich lipoproteins. Thus, the possibility that this female-specific homodimeric protein (Mr of subunit, 9500) is recognized by the oocyte receptor for low and very low density lipoproteins was investigated. ApoII was purified from very low density lipoproteins by a novel, rapid procedure and reconstituted with egg phosphatidylcholine (PC) by detergent-dialysis. The resulting discoidal apoII/PC lipoprotein particles contained 3 mg of apoII per mg of PC and had a buoyant density of 1.062 g/ml. The ability of apoII/PC, as well as of physiological particles containing apoII but devoid of apolipoprotein B (apoB), namely high density lipoproteins (HDL) from laying hens, to interact with the oocyte receptor was tested. Both of these ligands failed to show saturable high affinity binding, in contrast to the apoB-containing ligands, low and very low density lipoproteins. Furthermore, neither laying-hen HDL which contain apoII and apoA-I nor apoII/PC were able to displace receptor-bound apoB-containing lipoproteins, as shown in competitive binding assays as well as by ligand blotting. Thus, we conclude that apoB, but not apoII, participates in binding and uptake of very low density lipoproteins via receptor-mediated endocytosis by growing chicken oocytes.     

Characterization of lipoprotein particles isolated from the Golgi apparatus of rat liver

It has been proposed that particles within tubules and vesicles of the Golgi apparatus of liver cells are precursors of very low density lipoproteins in blood plasma. To characterize these particles we isolated a cell fraction rich in Golgi apparatus and associated particles from rat liver in quantities sufficient for analysis. Particles freed from the membranes of the Golgi apparatus and floated at d = 1.006 were studied by chemical analysis, immunodiffusion, and paper electrophoresis. The lipid composition of the Golgi particles was similar to that of very low density lipoproteins from the same rats. The protein content was about 10% of dry weight for both the Golgi particles and plasma very low density lipoproteins. The Golgi particles formed lines of identity with plasma very low density lipoproteins during immunodiffusion against antiserum to plasma very low density lipoproteins. On paper electrophoresis, however, many Golgi particles remained near the origin, with only a few migrating to the pre-beta position. It was concluded that the lipoproteins in the Golgi apparatus are the precursors of plasma very low density lipoproteins.     

Lipoprotein metabolism in the ovariectomized rat

The hyperlipoproteinemia observed after ovariectomy in rats was previously shown to be associated with increased concentrations of cholesterol, triglycerides, and apolipoproteins B, E, and C. In the present study, it was shown that increases in low density lipoproteins and high density lipoproteins were almost entirely responsible for the changes in plasma lipids and apolipoproteins after ovariectomy. The size of the low density lipoproteins and high density lipoproteins isolated from the plasma of ovariectomized rats as determined by agarose chromatography appeared to be somewhat different from that of control rats. Specifically, the apolipoprotein B appeared to be associated with somewhat smaller particles, whereas the apolipoprotein E from those rats appeared to be associated with larger particles than that of control rats. To determine the mechanism for the increased plasma low density lipoproteins, apolipoprotein B pool sizes and turnover rates were calculated and compared. In addition to an increased mass of low density lipoproteins in ovariectomized rats, the turnover rate of low density lipoproteins was increased almost twofold, indicating an increased low density lipoprotein synthesis and catabolism in those animals. We postulate that the increased low density lipoprotein levels of ovariectomized rats are due to an initial increased production of low density lipoproteins, followed by an enhanced catabolism of low density lipoproteins to establish a steady state at higher plasma low density lipoprotein concentrations.     

Overexpression of lipoprotein lipase in transgenic rabbits inhibits diet-induced hypercholesterolemia and atherosclerosis

Lipoprotein lipase (LPL) is a key enzyme in the hydrolysis of TG-rich lipoproteins. To elucidate the physiological roles of LPL in lipid and lipoprotein metabolism, we generated transgenic rabbits expressing human LPL. In postheparinized plasma of transgenic rabbits, the human LPL protein levels were about 650 ng/ml, and LPL enzymatic activity was found at levels up to 4-fold greater than that in nontransgenic littermates. Increased LPL activity in transgenic rabbits was associated with as much as an 80% decrease in plasma triglycerides and a 59% decrease in high density lipoprotein-cholesterol. Analysis of the lipoprotein density fractions revealed that increased expression of the LPL transgene resulted in a remarkable reduction in the level of very low density lipoproteins as well as in the level of intermediate density lipoproteins. In addition, LDL cholesterol levels in transgenic rabbits were significantly increased. When transgenic rabbits were fed a cholesterol-rich diet, the development of hypercholesterolemia and aortic atherosclerosis was dramatically suppressed in transgenic rabbits. These results demonstrate that systemically increased LPL activity functions in the metabolism of all classes of lipoproteins, thereby playing a crucial role in plasma triglyceride hydrolysis and lipoprotein conversion, and that overexpression of LPL protects against diet-induced hypercholesterolemia and atherosclerosis.     

Receptors for homologous plasma lipoproteins on a rat hepatoma cell line

Hepatocytes express on their surfaces more than one class of receptors capable of mediating the internalization of lipoproteins. However, relatively little is known about the binding characteristics of hepatic receptors for various lipoproteins, about the regulation of the receptors, and about the consequences for intracellular lipid metabolism of uptake of lipoproteins via different classes of receptors. The aim of the present studies was to characterize the binding and degradation of various lipoproteins and their mutual competition for cellular processing. Since these kinds of studies may be more easily carried out in continuous established hepatoma cell lines than in nondividing primary hepatocyte cultures, we examined the lipoprotein receptor functions of a well differentiated rat hepatoma (H-35). Cells were grown to confluence in Eagle's minimal essential medium in 15% newborn calf serum. Medium then was changed to 15% lipoprotein-deficient serum for 44 hr before experiments. External binding of 125I-labeled rat plasma and intestinal lymph lipoproteins was assessed at 4 degrees C. Cellular uptake and degradation were assessed at 37 degrees C. Lipoproteins were isolated by fixed angle or zonal ultracentrifugation or by heparin affinity column chromatography and characterized as to their lipid and apoprotein compositions. Labeled low density (LDL), high density (HDL2), non-apoE-HDL, very low density lipoproteins (VLDL), and chylomicron remnants (CM-R) each manifested specific and saturable binding and degradation by the hepatoma cells. Competition experiments indicated that separate receptors were present for LDL, HDL2, and CM-R. Most of HDL2 appeared to be bound to the non-apoE-HDL receptor.(ABSTRACT TRUNCATED AT 250 WORDS)     

Apolipoproteins of high, low, and very low density lipoproteins in human bile

We tested the hypothesis that apolipoproteins, the protein constituents of plasma lipoproteins, are secreted into bile. We examined human gallbladder bile obtained at surgery (N = 54) from subjects with (N = 44) and without (N = 10) gallstones and hepatic bile collected by T-tube drainage (N = 9) after cholecystectomy. Using specific radioimmunoassays for human apolipoproteins A-I and A-II, the major apoproteins of high density lipoproteins, for apolipoproteins C-II and C-III, major apoproteins of very low density lipoproteins, and for apolipoprotein B, the major apoprotein of low density lipoproteins, we found immunoreactivity for these five apolipoproteins in every bile sample studied in concentrations up to 10% of their plasma values. Using double immunodiffusion, we observed complete lines of identity between bile samples and purified apolipoproteins A-I, A-II, or C-II. Using molecular sieve chromatography, we found identical elution profiles for biliary apolipoproteins A-I, A-II and B and these same apolipoproteins purified from human plasma. When we added high density lipoproteins purified from human plasma to lipoprotein-free solutions perfusing isolated rat livers, we detected apolipoproteins A-I and A-II in bile. Similarly, when we added low density lipoproteins purified from human plasma to lipoprotein-free solutions perfusing isolated livers of rats treated with ethinyl estradiol in order to enhance hepatic uptake of low-density lipoproteins, we found apolipoprotein B in bile. These data indicate that apolipoproteins can be transported across the hepatocyte and secreted into bile.