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Proteome Map (proteome + map)
Selected AbstractsComparative proteomic analysis of primary mouse liver c-Kit,(CD45/TER119), stem/progenitor cellsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2007Yu-Fei He Abstract Liver stem/progenitor cells play a key role in liver development and maybe also in liver cancer development. In our previous study a population of c-Kit,(CD45/TER119), liver stem/progenitor cells in mouse fetal liver, was successfully sorted with large amount (106,107) by using immuno-magnetic microbeads. In this study, the sorted liver stem/progenitor cells were used for proteomic study. Proteins of the sorted liver stem/progenitor cells and unsorted fetal liver cells were investigated using two-dimensional electrophoresis. A two-dimensional proteome map of liver stem/progenitor cells was obtained for the first time. Proteins that exhibited significantly upregulation in liver stem/progenitor cells were identified by peptide mass fingerprinting and peptide sequencing. Nineteen protein spots corresponding to 12 different proteins were identified as showing significant upregulation in liver stem/progenitor cells and seem to play important roles in such cells in cell metabolism, cell cycle regulation, and stress. An interesting finding is that most of the upregulated proteins were overexpressed in various cancers (11 of 12, including 6 in human hepatocellular carcinoma (HCC)) and involved in cancer development as reported in previous studies. Some of the identified proteins were validated by real-time PCR, Western blotting, and immunostaining. Taken together, the data presented provide a significant new protein-level insight into the biology of liver stem/progenitor cells, a key population of cells that might be also involved in liver cancer development. J. Cell. Biochem. 102: 936,946, 2007. © 2007 Wiley-Liss, Inc. [source] Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolorMOLECULAR MICROBIOLOGY, Issue 4 2002A. R. Hesketh Summary The newly sequenced genome of Streptomyces coelicolor is estimated to encode 7825 theoretical proteins. We have mapped approximately 10% of the theoretical proteome experimentally using two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Products from 770 different genes were identified, and the types of proteins represented are discussed in terms of their anno-tated functional classes. An average of 1.2 proteins per gene was observed, indicating extensive post-translational regulation. Examples of modification by N-acetylation, adenylylation and proteolytic processing were characterized using mass spectrometry. Proteins from both primary and certain secondary metabolic pathways are strongly represented on the map, and a number of these enzymes were identified at more than one two-dimensional gel location. Post-translational modification mechanisms may therefore play a significant role in the regulation of these pathways. Unexpectedly, one of the enzymes for synthesis of the actinorhodin polyketide antibiotic appears to be located outside the cytoplasmic compartment, within the cell wall matrix. Of 20 gene clusters encoding enzymes characteristic of secondary metabolism, eight are represented on the proteome map, including three that specify the production of novel metabolites. This information will be valuable in the characterization of the new metabolites. [source] Yeast proteome map (update 2006)PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2007Michel Perrot Abstract To improve the potential of two-dimensional gel electrophoresis for proteomic investigations in yeast we have undertaken the systematic identification of Saccharomyces cerevisiae proteins separated on 2-D gels. We report here the identification of 187 novel protein spots. They were identified by two methods, mass spectrometry and gene inactivation. These identifications extend the number of protein spots identified on our yeast 2-D proteome map to 602, i.e. nearly half the detectable spots of the proteome map. These spots correspond to 417 different proteins. The reference map and the list of identified proteins can be accessed on the Yeast Protein Map server (www.ibgc.u-bordeaux2.fr/YPM). [source] From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applicationsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2007Uwe Plikat Dr. Abstract The hallmark of a systems biology approach is the integration of computational tools with experimental data encompassing multiple classes of biomolecules across different functional levels. Equally important as the availability of reasonably comprehensive information at the gene, protein, and metabolite levels is the development of adequate analysis and visualization tools to reduce the inherent complexity to interpretable dimensions. In this paper, we describe the integration of a 2-D gel-based proteome map of Staphylococcus aureus Mu50 with genomic and transcriptomic information through a customized data integration and user interface built on the Ensembl genome browser. We illustrate its application and potential through the analysis of a defined system perturbation caused by a mutation in the formyltransferase gene. We envision that this software package, which we called Insieme, can support the development of novel antibiotics by allowing a systems-based view of the bacterial response pathways. [source] Candidate antigens specifically detected by cerebrospinal fluid-IgG in oligoclonal IgG bands-positive multiple sclerosis patientsPROTEOMICS - CLINICAL APPLICATIONS, Issue 7 2007Masashi Nakamura Dr. Abstract The aim of the present study was to detect antigenic proteins that react specifically with cerebrospinal fluid (CSF)-IgG from oligoclonal IgG bands (OB)-positive multiple sclerosis (MS) patients. To identify such antigenic proteins, we developed a rat brain proteome map using 2-DE and applied it to the immunoscreening of brain proteins that react with CSF-IgG but not with serum-IgG in OB-positive MS patients. After sequential MALDI-TOF mass spectrometry, eight proteins [two neuronal proteins (tubulin ,-2 and , enolase-2), HSP-1, Tpi-1 protein and cellular enzymes (creatine kinase, phosphopyruvate hydratase, triosephosphate isomerase and phosphoglycerate kinase-1)] were identified as candidate antigens in seven MS patients. Reactivity to tubulin was seen in Western blotting in four patients, and CSF-specific anti-tubulin IgG was detected in one patient. In addition, CSF-specific anti-gamma enolase IgG was found in another patient. These findings suggest that intrathecal immune responses may occur against a broad range of proteins in MS. [source] A study of the antigenicity of Rickettsia helvetica proteins using two-dimensional gel electrophoresisAPMIS, Issue 4 2009NEDAA HAJEM Rickettsia helvetica is an obligate intracellular Gram-negative microorganism found in Ixodes ricinus ticks. When R. helvetica was first discovered in 1979, little was known about its physiology and it fell into oblivion until it recently was suspected of being pathogenic to humans. However, all efforts to isolate R. helvetica from patients have been unsuccessful, although serological responses against R. helvetica can be demonstrated. The aim of our study was to investigate the protein profile of R. helvetica and study the antigenicity of its proteins using two-dimensional (2D) immunoblot in order to characterize the immunological response against R. helvetica infection. Our results show that in addition to the known PS120 and OmpB antigenic R. helvetica proteins, three other antigens exist: a 60 kDa GroEL protein, a 10 kDa GroES protein and a hitherto unknown 35 kDa hypothetical protein that has similarities with ORF-RC0799 of Rickettsia conorii. Furthermore, the lipopolysaccharide showed strong antigenicity. In this study, we present the first proteome map and the first 2D immunoblot profile of R. helvetica and finally we present the 35 kDa R. helvetica as an additional antigen to the previously known rickettsial antigens. [source] Changes in the rat heart proteome induced by exercise training: Increased abundance of heat shock protein hsp20PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2006Marvin O. Boluyt Dr. Abstract Chronic exercise training elicits adaptations in the heart that improve pump function and confer cardioprotection. To identify molecular mechanisms by which exercise training stimulates this favorable phenotype, a proteomic approach was employed to detect rat cardiac proteins that were differentially expressed or modified after exercise training. Exercise-trained rats underwent six weeks of progressive treadmill training five days/week, 0%,grade, using an interval training protocol. Sedentary control rats were age- and weight-matched to the exercise-trained rats. Hearts were harvested at various times (0,72,h) after the last bout of exercise and were used to generate 2-D electrophoretic proteome maps and immunoblots. Compared with hearts of sedentary rats, 26,protein spot intensities were significantly altered in hypertrophied hearts of exercise-trained rats (p,<0.05), and 12,spots appeared exclusively on gels from hearts of exercise-trained rats. Immunoblotting confirmed that chronic exercise training, but not a single bout of exercise, elicited a ,2.5-fold increase in the abundance of one of the candidate proteins in the heart, a ,20,kDa heat shock protein (hsp20) that persisted for at least 72,h of detraining. Thus, exercise training alters the cardiac proteome of the rat heart; the changes include a marked increase in the expression of hsp20. [source] | ||||||||||