长双歧杆菌BBMN68 可溶性蛋白质图谱的建立

为了建立长双歧杆菌BBMN68蛋白质图谱,采用双向电泳的方法建立了2-D参考图谱,通过MALDI-TOF/MS质谱鉴定和数据库搜索,鉴定到206个蛋白质(占长双歧杆菌BBMN68基因预测总蛋白的11.4%)。通过2-D胶分析,共有800±15(对数期)和800±20(稳定期)个蛋白质,其中282个蛋白点成功鉴定,代表206个不同的蛋白质。另外,分析了实验鉴定蛋白质的等电点和分子量,蛋白功能,密码子偏好性,蛋白质疏水性以及蛋白质细胞定位的分析。研究结果为长双歧杆菌的比较蛋白质组学研究提供了参考图谱和蛋白质基础信息数据。     

长双歧杆菌NCC2705葡萄糖与果糖代谢的比较蛋白质组学

为揭示长双歧杆菌NCC2705 (Bifidobacterium longum NCC2705)果糖代谢途径, 建立其果糖发酵模型。以本实验室前期构建的长双歧杆菌NCC2705菌株蛋白质参考图谱为基础, 进行了果糖和葡萄糖生长的菌体比较蛋白质组学研究, 利用MALDI-TOF和ESI-MS/MS鉴定差异蛋白, 进一步通过半定量RT-PCR验证二者显著差异表达蛋白。果糖生长的菌体蛋白中鉴定到了所有葡萄糖降解途径中的酶和蛋白质, 另外鉴定到3倍以上差异蛋白点9个, 其对应的5个蛋白在果糖发酵中上调。半定量RT-PCR验证显著差异蛋白, 显示在果糖发酵中具有高水平表达是ABC 转运系统的果糖特异性-结合蛋白BL0033和ATP结合蛋白BL0034。果糖的发酵时间和浓度梯度试验显示诱导时间越长、浓度越高, BL0033的表达量越高。第一, 比较蛋白谱证明果糖和葡萄糖以相同途径降解。第二, BL0033的表达是受果糖诱导的, 果糖的吸收可能是通过一个特殊的转运系统, 即ABC转运系统将果糖从胞外转运到胞内, 其中BL0033和BL0034共同作为系统元件扮演了重要角色。     

长双歧杆菌NCC2705菌株应激蛋白的研究

研究长双歧杆菌NCC2705菌株发酵至稳定期时应激蛋白的表达情况。根据乳酸乳球菌IL1403菌株蛋白质参考图谱及长双歧杆菌NCC2705基因组注释中应激蛋白的分子量与等电点,确定应激蛋白在双向电泳凝胶上的相应蛋白点,并利用MALDI-TOF和/或ESI-MS/MS对相应蛋白质点进行鉴定。每个蛋白质点的肽指纹图谱均在长双歧杆菌NCC2705的蛋白质数据库用Mascot进行检索,共鉴定到44个蛋白点对应8个应激蛋白。这些蛋白为亲水性酸性蛋白,大多具有翻译后修饰现象,它们基因的CAI值除DnaJ外,其余均在0.5以上,在全细胞表达谱中为高丰度蛋白;此外,菌体具有较强的抗脂质过氧化和清除DPPH自由基的能力,而对羟自由基和超氧负离子的清除力较弱,推测鉴定到的具有逆转氧化损害作用的碱性过氧化氢还原酶(ahpC)可能是体内表达的降低氧损伤的主要酶。     

长双歧杆菌NCC2705葡萄糖与乳糖代谢的比较蛋白质组学

[目的]以本实验室前期构建的长双歧杆菌NCC2705菌株蛋白质参考图谱为基础,研究长双歧杆菌发酵乳糖和葡萄糖的比较蛋白质组学.[方法]采用ImageMaster 2D Elite Platnum Version 5.0比较分析3倍以上蛋白差异点;利用MALDI-TOF进行差异蛋白鉴定,每个蛋白质点的肽指纹图谱在长双歧杆菌NCC2705菌株的蛋白质数据库用Mascot进行检索;采用Pro-Q磷酸化试剂进行磷酸化蛋白的染色.[结果]鉴定到31个蛋白表达发生显著变化,在乳糖发酵中14个蛋白上调17个蛋白下调.这些蛋白为亲水性酸性蛋白,它们基因的CAI值均在0.5以上,主要包括糖代谢相关蛋白、应激蛋白、转录和翻译相关蛋白,还有一些未知功能的蛋白.此外,有两个蛋白:转醛缩酶(BL0715,transaldolase,tal)L3蛋白点和丙酮酸激酶(BL0988,pyruvate kinase,pyk)G9蛋白点发生了磷酸化作用.[结论]长双歧杆菌NCC2705在乳糖中生长快于葡萄糖,它们的降解途径是相同的;转醛缩酶和丙酮酸激酶发生了翻译后修饰作用,推测转醛缩酶在43T和47S发生了磷酸化,而丙酮酸激酶在65S发生了磷酸化.     

家蚕雌性附腺及其Ng突变体的蛋白质组差异研究(英)

家蚕雌蛾性附腺在化蛾前2到3天开始大量分泌胶状粘性蛋白,其贮存部迅速地膨大,而其Ng突变体的雌蛾性附腺不能正常分泌胶状粘性物质.分别对家蚕（Bombyx mori）的正常及Ng突变体雌蛾性附腺分泌部组织的蛋白质进行提取,并采用双向凝胶电泳和计算机辅助分析方法,对提取的蛋白质混合物进行分离和比较分析,并对主要差异表达的蛋白质用质谱鉴定.实验结果表明,用银染法,平均每张电泳图谱可以分离约700个蛋白质点,其中大部分的蛋白质点分布在pH 4～8 范围内,其分子质量主要集中在30～70 ku区域.比较分析发现一些差异表达蛋白,其中No2, 3蛋白质点经质谱鉴定为肌动蛋白A3,该蛋白质只在化蛹后期正常雌性附腺组织中特异表达,而Ng突变体中肌动蛋白A3的缺失,暗示了肌动蛋白A3可能与家蚕雌性附腺的胶状粘性物质的胞外分泌有关.     

转Bar基因甘蓝型油菜叶片蛋白质组变化的初步分析

采取SDS-PAGE与MALDI-TOF-MS联用的方法,对抗除草剂转Bar基因T1代甘蓝型油菜与普通栽培油菜的叶片蛋白质组进行比较性研究,获得差异蛋白质组的重要信息,并初步探讨差异蛋白的主要功能,以期找到与转Bar基因油菜抗除草剂有关的蛋白质,揭示其抗性机理.双向电泳表达图谱研究表明,Bar基因的转入使得转基因油菜中的差异蛋白表达质与量发生了显著变化,共得到16个发生差异表达的蛋白质点,其中11个经质谱分析功能得到鉴定,这些鉴定出的蛋白质涉及多个生理过程,如能量与代谢、信号转导、代谢相关蛋白离子转运和防御应答等.     

强休眠玉米种子休眠前后的蛋白差异表达

以强休眠玉米自交系08-641为试验材料,分别对处于休眠状态下的新鲜收获种子和经过10 d后熟作用破除休眠的种子进行了蛋白质组学差异表达分析。结果表明,通过双向电泳技术在3次重复试验下休眠状态的08-641鲜种子蛋白2-DE图谱上共检测到约600个蛋白质点,在经过10 d后熟作用破除休眠的08-641种子蛋白2-DE图谱上共检测到约620个蛋白质点,其中下调表达蛋白质点4个,上调表达蛋白质点4个,新增蛋白质点8个,缺失表达蛋白质点7个。经过质谱鉴定的差异表达蛋白质主要涉及球蛋白、胚胎晚期丰富蛋白、豆球蛋白等贮藏物蛋白质;蛋白酶体、山梨醇脱氢酶等参与物质代谢的蛋白质;热激蛋白等参与蛋白质结构、细胞功能调控的蛋白质。推测08-641种子休眠是由于种子内休眠相关蛋白的过量表达或缺失抑制了种子的正常萌发。     

不同分化程度的鼻咽癌细胞系质膜差异蛋白质组分析

本研究以CNE1和CNE2为材料,采用亚细胞蛋白质组研究方法研究不同分化程度鼻咽癌细胞系的差异蛋白质．首先用Percoll密度梯度离心法获得高纯度质膜,通过双向凝胶电泳分离、PDQuest软件分析后找出在肿瘤细胞中表达变化的蛋白质点,再用基质辅助激光解析电离飞行时间串联质谱（MALDI-TOF/TOF-MS）进行鉴定,共鉴定到9个具有2倍或2倍以上差异的蛋白质.这些表达差异的蛋白质参与了细胞分化、代谢及细胞信号传导过程．我们对其中5个蛋白质进行了实时定量PCR分析,对其中4个蛋白质的表达进行了免疫印迹验证．本试验为研究不同分化程度的鼻咽癌提供了一种蛋白质组研究方法,并且找到了galectin-1、annexin Ⅱ等一些可能与分化相关的蛋白质.这些数据对于研究鼻咽癌的生物学特性具有非常重要的意义．     

家蚕雌性附腺及其Ng突变体的蛋白质组差异研究

家蚕雌蛾性附腺在化蛾前2到3天开始大量分泌胶状粘性蛋白,其贮存部迅速地膨大,而其Ng突变体的雌蛾性附腺不能正常分泌胶状粘性物质.分别对家蚕(Bombyx mori)的正常及Ng突变体雌蛾性附腺分泌部组织的蛋白质进行提取,并采用双向凝胶电泳和计算机辅助分析方法,对提取的蛋白质混合物进行分离和比较分析,并对主要差异表达的蛋白质用质谱鉴定.实验结果表明,用银染法,平均每张电泳图谱可以分离约700个蛋白质点,其中大部分的蛋白质点分布在pH 4～8范围内,其分子质量主要集中在30～70 ku区域.比较分析发现一些差异表达蛋白,其中No2,3蛋白质点经质谱鉴定为肌动蛋白A3,该蛋白质只在化蛹后期正常雌性附腺组织中特异表达,而Ng突变体中肌动蛋白A3的缺失,暗示了肌动蛋白A3可能与家蚕雌性附腺的胶状粘性物质的胞外分泌有关.     

一株解淀粉芽孢杆菌生防蛋白的鉴定及分析

旨在鉴定一株拮抗葡萄霜霉病的解淀粉芽孢杆菌在NA液体培养基中的分泌蛋白中与生物防治相关的蛋白组分。采用蛋白质谱的方法对前期筛选到的一株拮抗葡萄霜霉病的解淀粉芽孢杆菌生防菌的在NA液体培养基中的分泌蛋白进行了鉴定。对鉴定到的蛋白采用基因本体论(GO)和京都基因与基因组百科全书(KEGG)的方法进行蛋白质组学分析,筛选与生物防治相关的蛋白。结果表明,从分泌蛋白中鉴定到了确定的53种蛋白质,其相对分子量大部分集中到0-100之间(占79.24%);涉及碳水化合物代谢、能量代谢、脂类代谢、氨基酸代谢和生物防御等过程,以及作为细胞组分参与结构组成。发现了6种参与植物与病原菌互作的蛋白,2种属于氨基肽酶家族,4种参与几丁质的生物降解过程。     

A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705

A comprehensive proteomic study was carried out to identify and characterize proteins expressed by Bifidobacterium longum NCC2705. A total of 708 spots representing 369 protein entries were identified by MALDI-TOF-MS and/or ESI-MS/MS. Isoelectric point values estimated by gel electrophoresis matched closely with their predicted ones, although some discrepancies exist suggesting that post-translational protein modifications might be common in B. longum. The identified proteins represent 21.4% of the predicted 1727 ORFs in the genome and correspond to 30% of the predicted proteome. Moreover 95 hypothetical proteins were experimentally identified. This is the first compilation of a proteomic reference map for the important probiotic organism B. longum NCC2705. The study aimed to define a number of cellular pathways related to important physiological processes at the proteomic level. Proteomic comparison of glucose- and fructose-grown cells revealed that fructose and glucose are catabolized via the same degradation pathway. Interestingly the sugar-binding protein specific to fructose (BL0033) and Frk showed higher levels of expression in cells grown on fructose than on glucose as determined by semiquantitative RT-PCR. BL0033 time course and concentration experiments showed that the induction time and fructose concentration correlates to increased expression of BL0033. At the same time, an ABC (ATP-binding cassette) transporter ATP-binding protein (BL0034) was slightly up-regulated in cells grown on fructose compared with glucose. All of the above results suggest that the uptake of fructose into the cell may be conducted by a specific transport system in which BL0033 might play an important role.     

A preliminary analysis of Bifidobacterium longum exported proteins by two-dimensional electrophoresis

Extracellular proteins of Bifidobacterium longum may mediate important interactions with the host. Here, we report on a comprehensive analysis of such proteins by using protein-free culture conditions and two-dimensional gel electrophoresis followed by mass spectrometry for protein identification. Seventeen proteins were detected in the culture supernatant, and 14 of them could be identified. Among these were 3 hypothetical solute-binding proteins of ABC transporters, an invasion-associated protein homolog, putative enzymes catalyzing cell wall turnover, several polypeptides with similarity to bacterial conjugation proteins, and 3 proteins of unknown function. Surprisingly, aldolase, usually considered as a cytoplasmic protein, was found in the culture supernatant. All proteins, excluding aldolase, were predicted to contain a signal peptide and a signal peptide cleavage site in their immature form. Some of the excreted proteins are interesting targets for further genetic and physiological studies.     

Differential analysis of protein expression of Bifidobacterium grown on different carbohydrates

We observed recently that colonic fermentation of lactose might be a major factor in the pathophysiology of lactose intolerance. Proteomic techniques could be helpful in interpreting the metabolic pathways of lactose fermentation. The objective of this study was to explore proteomic methodologies for studying bacterial lactose metabolism that can be used to detect and identify proteins associated with the onset of intolerance symptoms. Differential expression of cytoplasmic proteins of Bifidobacterium animalis, Bifidobacterium breve and Bifidobacterium longum grown on different carbohydrates (lactose, glucose, galactose) was analyzed with surface-enhanced laser desorption ionization-time of flight (SELDI-TOF) MS and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). After fractionation by SDS-PAGE, differentially-expressed proteins were identified with LC-MS/MS. The three strains grown on the same carbohydrate or the same strain grown on glucose or lactose showed differences in SELDI-TOF MS protein profiles. Differences in protein expression were observed in B. breve grown on glucose, galactose or lactose as analyzed with SDS-PAGE. With LC-MS/MS, proteins from Bifidobacterium were identified, which included enzymes for metabolism of lactose, glucose and galactose. In conclusion, the applied techniques can discern differences in protein expression of bacteria metabolizing different carbohydrates. These techniques are promising in studying metabolism of lactose and other substrates in a complex bacterial ecosystem such as the colonic microbiota.     

A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry

Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gut where they exert several health-promoting effects. The present paper reports the use of a strong cation exchange-reversed-phase-tandem mass spectrometry strategy to catalogue the most abundantly expressed proteins of a probiotic Bifidobacterium infantis strain. A global view of the B. infantis proteome was obtained. The bimodal representation of the proteins identified by mass spectrometry provides the first theoretical two-dimensional map of protein distribution for this organism. Among the 136 proteins identified by multidimensional protein identification technology (MudPIT) analysis, 118 showed the highest similarity with the translated sequences of B. longum genome, two proteins were similar to other Bifidobacterium species and the remaining 16 were similar to different genera. Specific biological activities have been assigned to 115 identified proteins, whereas 21 have been referred to the group of hypothetical proteins. The MudPIT approach allowed us to identify high mass and basic isoelectric point proteins that are generally challenging to visualize using the traditional two-dimensional electrophoresis technique. Redundancy in peptide and protein identification using the double chromatography technique was also evaluated.     

Changes induced by oxygen in rat liver proteins identified by high-resolution two-dimensional gel electrophoresis.

Molecular oxygen (O2) regulates the expression of a variety of genes. Several of the proteins that respond to changes in oxygen concentration have been identified in a variety of cell lines. We extend these previous studies by analyzing the effect of oxygen on the entire protein expression profile of an intact organ using high-resolution two-dimensional gel electrophoresis. To this end, we used an isolated, in vitro perfused organ preparation to produce two groups of rat livers perfused with high (95% O2, 5% CO2) or low (95% N2, 5% CO2) oxygen concentrations. Using two-dimensional gel electrophoresis we compared the protein expression profiles of both groups of livers. Computer analysis of the files obtained after laser densitometry of the two-dimensional gels revealed two spots that were strongly up-regulated in high PO2 perfused livers compared with low PO2 perfused livers. These spots were analyzed by peptide mass fingerprinting analysis. These spots were identified as arginase 1 (liver-type arginase; EC 3.5.3.1) and mitochondrial enoyl-CoA hydratase 1 (EC 4.2.1.17). The possible role of these proteins in its new context of oxygen availability is discussed.     

酸胁迫下短乳杆菌NCL912蛋白质的差异表达及其作用

【目的】本文从蛋白质组水平,对本实验室分离的一株高产γ-氨基丁酸的短乳杆菌NCL912(Lactobacillus brevis)在酸胁迫下蛋白质的差异表达及其应激机理进行探讨。【方法】利用双向凝胶电泳技术对pH 5.0和pH 4.0条件下,不含L-谷氨酸钠的培养物的蛋白质组电泳图谱进行了分析,并对酸胁迫下差异表达的蛋白进行了比较。利用质谱检测技术和生物信息学技术对这些差异表达的蛋白进行了鉴定、功能分类和代谢途径分析等。【结果】通过双向凝胶电泳技术,可以得到均匀、背景清晰、分辨率高、重复性好的Lb.brevis NCL912的双向凝胶电泳图谱。对pH 5.0和pH 4.0条件下培养的该菌总蛋白质电泳图谱进行比较,发现有25个差异表达的蛋白点。对这25个差异表达的蛋白进行了质谱鉴定。由于缺乏短乳杆菌NCL912的全基因组,所以其中只有8个蛋白点被质谱鉴定和分析得到。它们分别参与了蛋白质的合成、核苷酸的合成、糖酵解代谢、细胞能量水平的调节等。【结论】酸应激下这些表达蛋白质可通过其相应的功能来保护细胞耐受酸胁迫,从而使菌能够在酸性环境下生存增值。这可能就是Lb.brevis NCL912的酸胁迫应激机理之一。     

A reference map of a human pituitary adenoma proteome

In order to compare the proteomes from different cell types of pituitary adenomas for our long-term goal to clarify the molecular mechanisms that participate in the formation of pituitary adenoma, and to detect any tumor-related marker for an "early-stage" diagnosis, the two-dimensional gel electrophoresis (2-DE) reference map of a pituitary adenoma tissue proteome is described here. A vertical, two-dimensional (2-D) polyacrylamide gel electrophoresis system and PDQuest image analysis software have been used to provide a high level of between-gel reproducibility and to accurately array each protein expressed in a pituitary adenoma tissue. Mass spectrometry (matrix-assisted laser desorption/ionization-time of flight MALDI-TOF and liquid chromatography-electrospray ionization-quadrupole-ion trap LC-ESI-Q-IT) and protein databases were used to characterize each protein in the 2-D gel. The results demonstrate that a good reproducibility of the 2-D gel pattern was attained. The position deviation of matched spots among four 2-D gels was 1.95 +/- 0.45 mm in the isoelectric focusing direction, and 1.70 +/- 0.53 mm in the sodium dodecyl sulfate-polyacrylamide gel electrophoresis direction. A total of ca. 1000 protein spots were separated by 2-DE, and 135 protein spots that represent 111 proteins were characterized with mass spectrometry (96 spots for MALDI-TOF, 39 spots for LC-ESI-Q-IT). The characterized proteins include pituitary hormones, cellular signals, enzymes, cellular-defense proteins, cell-structure proteins, transport proteins, etc. Those proteins were located in the cytoplasmic, cellular membrane, mitochondrial, endoplasmic reticulum, nuclear, ribonucleosome, extracellular fractions, or were secreted in plasma, etc. Those identified proteins contribute to a functional profile of the pituitary adenoma proteome. These data will be used to expand the proteome database of the human pituitary, which can be accessed in the website http://www.utmem.edu /proteomics.     

Effect of heat-shock and bile salts on protein synthesis of Bifidobacterium longum revealed by [35S]methionine labelling and two-dimensional gel electrophoresis

Experimental conditions for efficient protein radiolabelling and two-dimensional gel electrophoresis were developed for Bifidobacterium longum. Using these tools, protein synthesis in cells before and after heat-shock and bile salts treatment was investigated. Following heat-stress, 13 proteins were upregulated, of which HtrA, DnaK and GroEL were also moderately induced by bile salts, indicating close relationship between the heat and bile salts responses in bifidobacteria. Our work indicated that, as a consequence of prolonged heat-stress, HtrA undergoes sequential modification and proteolysis, and that this mechanism could be employed by bifidobacteria to respond to heat-stress.