Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences

Separation of proteins by two-dimensional gel electrophoresis (2-DE) coupled with identification of proteins through peptide mass fingerprinting (PMF) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn) constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.     

Predominant identification of RNA-binding proteins in Fas-induced apoptosis by proteome analysis

Proteome analysis of Jurkat T cells was performed in order to identify proteins that are modified during apoptosis. Subtractive analysis of two-dimensional gel patterns of apoptotic and nonapoptotic cells revealed differences in 45 protein spots. 37 protein spots of 21 different proteins were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry. The hnRNPs A0, A2/B1, A3, K, and R; the splicing factors p54(nrb), SRp30c, ASF-2, and KH-type splicing regulatory protein (FUSE-binding protein 2); and alpha NAC, NS1-associated protein 1, and poly(A)-binding protein 4 were hitherto unknown to be involved in apoptosis. The putative cleavage sites of the majority of the proteins could be calculated by the molecular masses and isoelectric points in the two-dimensional electrophoresis gel, the peptide mass fingerprints, and after translation by treatment with recombinant caspase-3. Remarkably, 15 of the 21 identified proteins contained the RNP or KH motif, the best characterized RNA-binding motifs.     

Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data

As an initial step to the comprehensive proteomic analysis of Panax ginseng C. A. Meyer, protein mixtures extracted from the cultured hairy root of Panax ginseng were separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). The protein spots were analyzed and identified by peptide finger printing and internal amino acid sequencing by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and electrospray ionization quadrupole-time of flight mass spectrometry (ESI Q-TOF MS), respectively. More than 300 protein spots were detected on silver stained two-dimensional (2-D) gels using pH 3-10, 4-7, and 4.5-5.5 gradients. Major protein spots (159) were analyzed by peptide fingerprinting or de novo sequencing and the functions of 91 of these proteins were identified. Protein identification was achieved using the expressed sequence tag (EST) database from Panax ginseng and the protein database of plants like Arabidopsis thaliana and Oryza sativa. However, peptide mass fingerprinting by MALDI-TOF MS alone was insufficient for protein identification because of the lack of a genome database for Panax ginseng. Only 17 of the 159 protein spots were verified by peptide mass fingerprinting using MALDI-TOF MS whereas 87 out of 102 protein spots, which included 13 of the 17 proteins identified by MALDI-TOF MS, were identified by internal amino acid sequencing using tandem mass spectrometry analysis by ESI Q-TOF MS. When the internal amino acid sequences were used as identification markers, the identification rate exceeded 85.3%, suggesting that a combination of internal sequencing and EST data analysis was an efficient identification method for proteome analysis of plants having incomplete genome data like ginseng. The 2-D patterns of the main root and leaves of Panax ginseng differed from that of the cultured hairy root, suggesting that some proteins are exclusively expressed by different tissues for specific cellular functions. Proteome analysis will undoubtedly be helpful for understanding the physiology of Panax ginseng.     

Proteome analysis of hepatocellular carcinoma cell strains, MHCC97-H and MHCC97-L, with different metastasis potentials

To better understand the mechanism underlying hepatocellular carcinoma (HCC) metastasis and to search for potential markers for HCC prognosis, differential proteome analysis on two HCC cell strains with high and low metastatic potentials, MHCC97-H and MHCC97-L, was conducted using two-dimensional (2-D) gel electrophoresis followed by matrix-assisted laser desorption/time of flight mass spectrometry and liquid chromatography ion trap mass spectrometry. Image analysis of silver-stained 2-D gels revealed that 56 protein spots showed significant differential expression in MHCC97-H and MHCC97-L cells (Student's t-test, P < 0.05) and 4 protein spots were only detected in MHCC97-H cells. Fourteen protein spots were further identified using in-gel tryptic digestion, peptide mass fingerprinting and tandem mass spectrometry. The expressions of pyruvate kinase M2, ubiquitin carboxy-terminal hydrolase L1, laminin receptor 67 kDa, S100 calcium-binding protein A4, thioredoxin and cytokeratin 19 were elevated in MHCC97-H cells. However, manganese superoxide dismutase, calreticulin precursor, cathepsin D, lactate dehydrogenase B, non-metastatic cell protein 1, cofilin 1 and calumenin precursor were down-regulated in MHCC97-H cells. Intriguingly, most of these identified proteins have been reported to be associated with tumor metastasis. The functional implications of alterations in the levels of these proteins are discussed.     

Proteomic analysis of peripheral blood mononuclear cells: selective protein processing observed in patients with rheumatoid arthritis

In a comparative proteome analysis of peripheral blood mononuclear cells (PBMCs), we analyzed 130 two-dimensional gels obtained from 33 healthy control individuals and 32 patients diagnosed with rheumatoid arthritis (RA). We found 16 protein spots that are deregulated in patients with RA and, using peptide mass fingerprinting and Western blot analyses, identified these spots as belonging to 9 distinct proteins. A hierarchical clustering procedure organizes the study subjects into two main clusters based on the expression of these 16 protein spots, one that contains mostly healthy control individuals and the other mostly RA patients. The majority of the proteins differentially expressed in RA patients when compared with healthy controls can be detected as protein fragments in PBMCs obtained from RA patients. This set of deregulated proteins includes several factors that have been shown to be autoantigens in autoimmune diseases.     

Distinct tumor cell membrane constituents activate human monocytes for tumor necrosis factor synthesis

Several lines of evidence point to an activation mechanism of monocytes/macrophages by tumor cells. In this study we present data for distinct surface structures on K562 and Jurkat cells to directly induce TNF-mRNA expression and TNF production by human peripheral blood monocytes. Northern analysis showed that incubation of monocytes with either K562 or Jurkat cells led to a significant increase in TNF-mRNA expression. In addition, enhanced TNF production was detected in supernatants of monocyte cultures activated by Jurkat cells. Not only viable tumor cells but also metabolically inactivated tumor cells, cytoblasts, and membrane preparations from Jurkat and K562 cells induced TNF-mRNA expression. We identified two different membrane protein fractions with relative molecular mass of 32 to 38 kDa for Jurkat cells and 46 to 54 kDa for K562 cells that were responsible for monocyte activation.     

Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data

Proteins separated by two-dimensional gel electrophoresis (2-DE) may be distributed over several spots. Otherwise, one spot may contain more than one component. The same protein occurring in several spots supposedly represents differently modified protein species that might be of biological relevance. Identification of spots with peptide mass fingerprinting and database searching leads only to the detection of the major spot components. If a spot also contains additional minor protein components, quantitation of spots with protein staining techniques or antibody detection becomes misleading. In order to find spots containing minor components we applied correspondence analysis, a multivariate data exploration method, to peptide mass fingerprint data. Correspondence analysis using peak lists revealed groups of spots containing the same protein with their characteristic mass-to-charge ratio (m/z) values. In order to detect different protein spot components an interactive threshold setting and removal of m/z values with subsequent recalculation of the correspondence analysis using our software tool CorrAn are performed. The usefulness of this methodical approach was shown by a data set of peptide mass fingerprints of 284 spots of Helicobacter pylori 26695 separated by 2-DE.     

Bacillus subtilis自然感受态缺陷株蛋白质表达谱的初步分析

利用蛋白质双向电泳对枯草芽孢杆菌自然感受态缺陷突变株BR151pm感受态形成期的全细胞蛋白质进行比较分析,发现有28个蛋白质斑点出现变化。利用基质辅助激光解析/电离串联飞行时间质谱对其巾2个明显缺失的蛋白斑点进行分析鉴定,确定这2个蛋白质分别为直接参与自然感受态形成的Nin蛋白和RecA蛋白,进一步确证了BR151pm为自然感受态缺陷突变株。     

外源性VEGF对结肠癌细胞SW480蛋白质变化的影响

利用RT-PCR发现结肠癌细胞存在血管内皮生长因子(VEGF)及其受体(VEGFR)的表达,随后采用外源性VEGF对结肠癌细胞SW480进行体外刺激,流式细胞仪检测到结肠癌细胞刺激后快速进入分裂期,同时提取VEGF作用前后的结肠癌细胞总蛋白,蛋白质组学研究,发现存在明显的蛋白质变化,其中鉴定出10个差异蛋白质.提示外源性VEGF可以促进结肠癌细胞增殖并对肿瘤细胞蛋白质组产生明显的影响.     

K562耐药细胞的建立及相关蛋白表达改变的研究

为研究肿瘤细胞发生多药耐药后蛋白整体水平表达的改变,将K562细胞与阿霉素(ADR)共同培养,逐渐增加药物浓度,最后建立耐阿霉素的细胞K562／ADR株。MTT法检测阿霉素(ADR)、顺铂(DDP)、5-氟尿嘧啶(5-FU)和长春新碱(VCR)对K562和K562／ADR细胞的半数抑制率(IC50)。利用蛋白质组学技术,通过双向凝胶电泳分离K562和K562／ADR细胞的总蛋白,银染显色,分析差异蛋白,对部分蛋白点进行胶内酶解,用基质辅助激光解析飞行时间质谱法得肽质量指纹图谱,用AutoMS-Fit软件查询NCBInr数据库鉴定蛋白质。结果表明K562细胞经ADR诱导后出现多药耐药现象,ADR、DDP、5-FU和VCR对K562／ADR细胞的IC50明显高于K562。将K562和K562／ADR的双向电泳图谱进行差异比较,初步鉴定仅在K562／ADR图谱上出现的蛋白是一些与细胞分裂、基因转录有关的蛋白质。这些蛋白的变化与耐药细胞的特性相关,可能与临床化疗的多药耐药现象有联系。     

K562耐药细胞的建立及相关蛋白表达改变的研究

为研究肿瘤细胞发生多药耐药后蛋白整体水平表达的改变,将K562细胞与阿霉素(ADR)共同培养,逐渐增加药物浓度,最后建立耐阿霉素的细胞K562/ADR株。MTT法检测阿霉素(ADR)、顺铂(DDP)、5-氟尿嘧啶(5-FU)和长春新碱(VCR)对K562和K562/ADR细胞的半数抑制率(IC_(50))。利用蛋白质组学技术,通过双向凝胶电泳分离K562和K562/ADR细胞的总蛋白,银染显色,分析差异蛋白,对部分蛋白点进行胶内酶解,用基质辅助激光解析飞行时间质谱法得肽质量指纹图谱,用AutoMS-Fit软件查询NCBInr数据库鉴定蛋白质。结果表明K562细胞经ADR诱导后出现多药耐药现象,ADR、DDP、5-FU和VCR对K562/ADR细胞的IC_(50)明显高于K562。将K562和K562/ADR的双向电泳图谱进行差异比较,初步鉴定仅在K562/ADR图谱上出现的蛋白是一些与细胞分裂、基因转录有关的蛋白质。这些蛋白的变化与耐药细胞的特性相关,可能与临床化疗的多药耐药现象有联系。     

Overexpression of sorcin in multidrug resistant human leukemia cells and its role in regulating cell apoptosis

In an attempt to identify novel proteins involved in the emergence of multidrug resistance (MDR) in leukemia cells, we adopted a proteomics approach to analyze protein expression patterns in leukemia cell lines, K562, and its MDR counterpart, K562/A02. Combining high-resolution two-dimensional gel electrophoresis and mass spectrometry, we compared the protein expression profiles between K562 and K562/A02. A total number of 22 protein spots with altered abundances of more than 2-fold were detected and 14 proteins were successfully identified. Consistent with our previous observations by cDNA microarray, sorcin, a 22-kDa calcium-binding protein, was also identified by this proteomic approach with a 10.4-fold up-regulation in K562/A02 cells. Overexpression of sorcin protein in K562 cells by gene transfection led to significantly reduced cytosolic calcium level and increased resistance to cell apoptosis. Further, leukemia cell lines over-expressing sorcin also showed up-regulation of Bcl-2, along with decreased level of Bax. Taken together, our results suggest that sorcin plays an important role in the emergence of MDR in leukemia cells via regulating cell apoptosis pathways, thus may represent both a new MDR marker for prognosis and a good target for anti-MDR drug development.     

Bacillus subtilis自然感受态缺陷株蛋白质表达谱的初步分析

利用蛋白质双向电泳对枯草芽孢杆菌自然感受态缺陷突变株BR151pm感受态形成期的全细胞蛋白质进行比较分析,发现有28个蛋白质斑点出现变化。利用基质辅助激光解析/电离串联飞行时间质谱对其巾2个明显缺失的蛋白斑点进行分析鉴定,确定这2个蛋白质分别为直接参与自然感受态形成的Nin蛋白和RecA蛋白,进一步确证了BR151pm为自然感受态缺陷突变株。     

Bacillus subtilis自然感受态缺陷株蛋白质表达谱的初步分析

利用蛋白质双向电泳对枯草芽孢杆菌自然感受态缺陷突变株BR151pm感受态形成期的全细胞蛋白质进行比较分析,发现有28个蛋白质斑点出现变化。利用基质辅助激光解析/电离串联飞行时间质谱对其巾2个明显缺失的蛋白斑点进行分析鉴定,确定这2个蛋白质分别为直接参与自然感受态形成的Nin蛋白和RecA蛋白,进一步确证了BR151pm为自然感受态缺陷突变株。     

Proteomic analysis of rat heart in ischemia and ischemia-reperfusion using fluorescence two-dimensional difference gel electrophoresis

Ischemia-reperfusion injury is a major complication occurring in acute myocardial infarction, cardiopulmonary bypass surgery, and heart transplantation. The aim of this study was to identify proteins that were involved in ischemia-reperfusion injury using fluorescence two-dimensional difference gel electrophoresis. We compared the 100,000 x g precipitate fractions of normal, ischemic and ischemia-reperfused rat hearts and detected six spots which changed more than two-fold in expression level and two additional spots related to these spots. Using peptide mass fingerprinting by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, we identified five of these spots as protein disulfide isomerase A3 (PDA3), one as 60 kDa heat shock protein (HSP60) and two as elongation factor Tu (EF-Tu). HSP60 was increased during ischemia and decreased to normal expression level after reperfusion. EF-Tu was increased in ischemia but not decreased by reperfusion. We also found that several protein spots of PDA3 shifted towards a higher isoelectric point in ischemia and ischemia-reperfusion. Our data strongly suggested that PDA3 underwent dephosphorylation during ischemia and reperfusion and serine 343 of PDA3 was one of the phosphorylation sites.     

Proteome analysis on an early transformed human bronchial epithelial cell line,BEP2D,after alpha-particle irradiation

To probe the mechanism of carcinogenesis of lung cancer at the molecular level and to find potential protein markers involved in the early phase of tumorgenesis, differential proteome analysis on primary passage cell line R15H, and early transformed cell line R15H20 derived from (238)Pu alpha-particle irradiation of human papillomavirus (HPV) 18-immortalized human bronchial epithelial cell line (BEP2D), was carried out using two-dimensional electrophoresis (2-DE) and peptide mass fingerprinting (PMF) with matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. Image analysis and Student's t-test (p < 0.05) showed that three protein spots were only expressed in R15H, intensities of 43 protein spots on the gels were altered between R15H and R15H20. Two of the three spots that were only expressed in R15H were identified as high mobility group protein 1. Two proteins decreased in abundance in R15H20 were identified as maspin precursor, a tumor suppressor and aminoacylase-1. Ornithine aminotransferase and peptidyl-prolyl cis-trans isomerase A that were increased in R15H20, were also identified. Relationships between these differentially expressed proteins and the carcinogenesis mechanism of lung cancer are discussed. The protein expression profile of the R15H cell line was also constructed during the study as a reference map for further comparative proteome analysis of the irradiation induced BEP2D cell line. Of the 90 spots analyzed with PMF in the 2-DE gel of R15H cell line, 50 proteins were identified by searching the nonredundant protein database SWISS-PROT/TrEMBL.     

A proteomic analysis of allograft rejection in rats after liver transplantation

In order to understand the allograft rejection in orthotopic liver transplantation (OLT), an allograft rejection rat model was established and studied by proteomic approach. The protein expression profiles of liver tissues were acquired by fluorescence two-dimensional difference gel electrophoresis (2D DIGE) that incorporated a pooled internal standard and reverse fluorescent labeling method. The expression levels of 27 protein spots showed significant changes in acute rejection rats. Among these spots, 19 were identified with peptide mass fingerprinting using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) after tryptic in-gel digestion. The results of the present paper could be helpful for our better understanding of allograft rejection in organ transplantation.