201
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Breikers G, van Breda SGJ, Bouwman FG, van Herwijnen MHM, Renes J, Mariman ECM, Kleinjans JCS, van Delft JHM. Potential protein markers for nutritional health effects on colorectal cancer in the mouse as revealed by proteomics analysis. Proteomics 2006; 6:2844-52. [PMID: 16596712 DOI: 10.1002/pmic.200500067] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
It is suggested that colorectal cancer might be prevented by changes in diet, and vegetable consumption has been demonstrated to have a protective effect. Until now, little is known about the effects of vegetable consumption at the proteome level. Therefore, the effect of increased vegetable intake on the protein expression in the colonic mucosa of healthy mice was studied. Aim was to identify the proteins that are differentially expressed by increased vegetable consumption and to discriminate their possible role in the protection against colorectal cancer. Mice were fed four different vegetable diets, which was followed by analysis of total cellular protein from colonic mucosal cells by a combination of 2-DE and MS. We found 30 proteins that were differentially expressed in one or more diets as compared to the control diet. Six could be identified by MALDI-TOF MS: myosin regulatory light chain 2, carbonic anhydrase I, high-mobility group protein 1, pancreatitis-associated protein 3, glyceraldehyde-3-phosphate dehydrogenase and ATP synthase oligomycin sensitivity conferral protein. Alterations in the levels of these proteins agree with a role in the protection against colon cancer. We conclude that these proteins are suitable markers for the health effect of food on cancer. The observed altered protein levels therefore provide support for the protective effects of vegetables against colorectal cancer.
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Affiliation(s)
- Githa Breikers
- Department of Health Risk Analysis and Toxicology, Maastricht University, Maastricht, The Netherlands
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202
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Ottens AK, Kobeissy FH, Golden EC, Zhang Z, Haskins WE, Chen SS, Hayes RL, Wang KKW, Denslow ND. Neuroproteomics in neurotrauma. MASS SPECTROMETRY REVIEWS 2006; 25:380-408. [PMID: 16498609 DOI: 10.1002/mas.20073] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Neurotrauma in the form of traumatic brain injury (TBI) afflicts more Americans annually than Alzheimer's and Parkinson's disease combined, yet few researchers have used neuroproteomics to investigate the underlying complex molecular events that exacerbate TBI. Discussed in this review is the methodology needed to explore the neurotrauma proteome-from the types of samples used to the mass spectrometry identification and quantification techniques available. This neuroproteomics survey presents a framework for large-scale protein research in neurotrauma, as applied for immediate TBI biomarker discovery and the far-reaching systems biology understanding of how the brain responds to trauma. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of neurotrauma on society.
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Affiliation(s)
- Andrew K Ottens
- Center of Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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203
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Nägele E, Vollmer M, Hörth P, Vad C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev Proteomics 2006; 1:37-46. [PMID: 15966797 DOI: 10.1586/14789450.1.1.37] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Today, 2D online or offline liquid chromatography/mass spectrometry is state of the art for the identification of proteins from complex proteome samples in many laboratories. Both 2D liquid chromatography methods use two orthogonal liquid chromatography separation techniques. The most commonly used techniques are strong cation exchange chromatography for the first dimension and reversed phase separation for the second dimension. In order to improve sensitivity the reversed phase separation is usually performed in the nanoflow scale and mass spectrometry is used as the final detection method. The high-performance liquid chromatography techniques complement the 2D-gel techniques supporting their weaknesses. This is especially true for the gel separation of hydrophobic membrane proteins, which play an important role in living cells as well as being important targets for future pharmaceutical drugs.
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Affiliation(s)
- Edgar Nägele
- Agilent Technologies, R&D and Marketing GmbH & Co. KG, Hewlett-Packard-Str. 8, Waldbronn, Germany.
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204
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Shamseldin A, Nyalwidhe J, Werner D. A proteomic approach towards the analysis of salt tolerance in Rhizobium etli and Sinorhizobium meliloti strains. Curr Microbiol 2006; 52:333-9. [PMID: 16604415 DOI: 10.1007/s00284-005-6472-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 09/25/2005] [Indexed: 11/24/2022]
Abstract
Soluble proteins from the salt-tolerant Rhizobium etli strain EBRI 26 were separated by two-dimensional (2D) gel electrophoresis and visualised by Commassie staining. Six proteins are highly expressed after induction by 4% NaCl compared to the non-salt-stressed cells. These proteins have pI between 5 and 5.5 and masses of approximately 22, 25, 40, 65, 70, and 95 kDa. These proteins were analysed by Matrix-assisted laser adsorption ionization time of flight (MALDI-TOF) after digestion with trypsin. Despite having very good peptide mass fingerprint data, these proteins could not be identified, because the genome sequence of R. etli is not yet published. In a second approach, soluble proteins from salt-induced or non-salt-induced cultures from R. etli strain EBRI 26 were separately labelled with different fluorescent cyano-dyes prior to 2D difference in gel electrophoresis. Results revealed that 49 proteins are differentially expressed after the addition of sodium chloride. Fourteen proteins are overexpressed and 35 were downregulated. The genome of Sinorhizobium meliloti, a closely related species to R. etli, has been published. Similar experiments using Sinorhizobium meliloti strain 2011 identified four overexpressed and six downregulated proteins. Among the overexpressed protein is a carboxynospermidin decarboxylase, which plays an important role in the biosynthesis of spermidin (polyamine). The enzyme catalase is among the downregulated proteins. These proteins may play a role in salt tolerance.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, Mubarak City for Scientific Research and Technological Applications, New Borg El-Arab, Alexandria, Egypt
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205
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Jin LT, Hwang SY, Yoo GS, Choi JK. A mass spectrometry compatible silver staining method for protein incorporating a new silver sensitizer in sodium dodecyl sulfate-polyacrylamide electrophoresis gels. Proteomics 2006; 6:2334-7. [PMID: 16493709 DOI: 10.1002/pmic.200500596] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A quick, sensitive, and MALDI-TOF MS compatible silver staining method, namely Eriochrome black T (EBT)-silver method, is described. The method can detect 0.05-0.2 ng protein within 60 min in SDS-PAGE gels. EBT dye was used as a silver ion sensitizer having reducing power for silver ions.
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Affiliation(s)
- Li-Tai Jin
- College of Pharmacy, Chonnam National University, Kwangju, South Korea
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206
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Horecka J, Charter NW, Bosano BL, Fung P, Kobel P, Peng K, Eglen RM. Antibody-free method for protein detection on blots using enzyme fragment complementation. Biotechniques 2006; 40:381-3. [PMID: 16568826 DOI: 10.2144/000112119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Joe Horecka
- DiscoveRx Corporation, Fremont, CA 94538, USA
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207
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Glinski M, Weckwerth W. The role of mass spectrometry in plant systems biology. MASS SPECTROMETRY REVIEWS 2006; 25:173-214. [PMID: 16284938 DOI: 10.1002/mas.20063] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.
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Affiliation(s)
- Mirko Glinski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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208
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Vemuri GN, Aristidou AA. Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev 2006; 69:197-216. [PMID: 15944454 PMCID: PMC1197421 DOI: 10.1128/mmbr.69.2.197-216.2005] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The importance of regulatory control in metabolic processes is widely acknowledged, and several enquiries (both local and global) are being made in understanding regulation at various levels of the metabolic hierarchy. The wealth of biological information has enabled identifying the individual components (genes, proteins, and metabolites) of a biological system, and we are now in a position to understand the interactions between these components. Since phenotype is the net result of these interactions, it is immensely important to elucidate them not only for an integrated understanding of physiology, but also for practical applications of using biological systems as cell factories. We present some of the recent "-omics" approaches that have expanded our understanding of regulation at the gene, protein, and metabolite level, followed by analysis of the impact of this progress on the advancement of metabolic engineering. Although this review is by no means exhaustive, we attempt to convey our ideology that combining global information from various levels of metabolic hierarchy is absolutely essential in understanding and subsequently predicting the relationship between changes in gene expression and the resulting phenotype. The ultimate aim of this review is to provide metabolic engineers with an overview of recent advances in complementary aspects of regulation at the gene, protein, and metabolite level and those involved in fundamental research with potential hurdles in the path to implementing their discoveries in practical applications.
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Affiliation(s)
- Goutham N Vemuri
- Center for Molecular BioEngineering, Drifmier Engineering Center, University of Georgia, Athens, 30605, USA
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209
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Hsu J, Chang SJ, Franz AH. MALDI-TOF and ESI-MS analysis of oligosaccharides labeled with a new multifunctional oligosaccharide tag. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:194-204. [PMID: 16406228 DOI: 10.1016/j.jasms.2005.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 10/18/2005] [Accepted: 10/20/2005] [Indexed: 05/06/2023]
Abstract
A new multifunctional oligosaccharide label with a 1 degree amino-group was synthesized and characterized. The oligosaccharide label was introduced into several neutral oligosaccharides by reductive amination, and the derivatives were analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) and by electrospray ionization (ESI) mass spectrometry. It was demonstrated that the labeling reaction was satisfactory, and that as little as 50 pmol of starting material could be efficiently labeled with minimal loss to side reactions. A mixture of high-mannose N-glycans released from ribonuclease B was labeled. The label did not appear to interfere with structural characterization of the oligosaccharides by mass spectrometry. N-quaternization of the labeled oligosaccharides resulted in significantly increased sensitivity of detection with as little as 100 fmol on the probe detected. Deuterium coding of labeled oligosaccharide mixtures and relative abundance of mixture components was investigated. A protocol for the chromatographic separation of mixtures of labeled oligosaccharides by HPLC was developed and is reported here.
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Affiliation(s)
- Joanne Hsu
- Department of Chemistry, University of the Pacific, Stockton, California 95211, USA
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210
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Agrawal GK, Rakwal R. Rice proteomics: a cornerstone for cereal food crop proteomes. MASS SPECTROMETRY REVIEWS 2006; 25:1-53. [PMID: 15957154 DOI: 10.1002/mas.20056] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proteomics-a systematic study of proteins present in a cell, tissue, organ, or organism at a particular moment during the life cycle-that began with classical two-dimensional electrophoresis and its advancement during the 1990s, has been revolutionized by a series of tremendous technological developments in mass spectrometry (MS), a core technology. Proteomics is exerting its influence on biological function of genes and genomes in the era (21st century) of functional genomics, and for this reason yeast, bacterial, and mammalian systems are the best examples. Although plant proteomics is still in its infancy, evolving proteomic technologies and the availability of the genome sequences of Arabidopsis thaliana (L.) Heyhn, and rice (Oryza sativa L.), model dicotyledoneous and monocotyledoneous (monocot) species, respectively, are propelling it towards new heights, as evidenced by the rapid spurt in worldwide plant proteome research. Rice, with an immense socio-economic impact on human civilization, is a representative model of cereal food crops, and we consider it as a cornerstone for functional genomics of cereal plants. In this review, we look at the history and the current state of monocot proteomes, including barley, maize, and wheat, with a central focus on rice, which has the most extensive proteomic coverage to date. On one side, we highlight advances in technologies that have generated enormous amount of interest in plant proteomics, and the other side summarizes the achievements made towards establishing proteomes during plant growth & development and challenge to environmental factors, including disease, and for studying genetic relationships. In light of what we have learned from the proteomic journey in rice and other monocots, we finally reveal and assess their impact in our continuous strive towards completion of their full proteomes.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Agricultural Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.
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211
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Roque ACA, Lowe CR. Advances and applications of de novo designed affinity ligands in proteomics. Biotechnol Adv 2006; 24:17-26. [PMID: 16006085 DOI: 10.1016/j.biotechadv.2005.05.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 05/09/2005] [Indexed: 11/30/2022]
Abstract
Affinity chromatography represents a promising technique for decoding the proteomics universe. While conventional affinity purification is being used in conjunction with two-dimensional electrophoresis (2D-PAGE) and mass spectrometry (MS) for the study of proteomes and subproteomes, scientists are still confronted with the need for specific and tailor-made affinity ligands to target desired groups and families of proteins. Evidence has shown that, in many situations, synthetic affinity ligands can circumvent inconveniences associated with the utilisation of biological ligands for the chromatography-based purification of biomolecules. This review will highlight the potential applications of affinity chromatography and synthetic de novo designed ligands as separation tools for proteomics.
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212
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Kolkman A, Slijper M, Heck AJR. Development and application of proteomics technologies in Saccharomyces cerevisiae. Trends Biotechnol 2005; 23:598-604. [PMID: 16202464 DOI: 10.1016/j.tibtech.2005.09.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/18/2005] [Accepted: 09/19/2005] [Indexed: 11/21/2022]
Abstract
Proteomics research focuses on the identification and quantification of "all" proteins present in cells, organisms or tissue. Proteomics is technically complicated because it encompasses the characterization and functional analysis of all proteins that are expressed by a genome. Moreover, because the expression levels of proteins strongly depend on complex regulatory systems, the proteome is highly dynamic. This review focuses on the two major proteomics methodologies, one based on 2D gel electrophoresis and the other based on liquid chromatography coupled to mass spectrometry. The recent developments of these methodologies and their application to quantitative proteomics are described. The model system Saccharomyces cerevisiae is considered to be the optimal vehicle for proteomics and we review studies investigating yeast adaptation to changes in (nutritional) environment.
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Affiliation(s)
- Annemieke Kolkman
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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213
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Agrawal GK, Thelen JJ. Development of a simplified, economical polyacrylamide gel staining protocol for phosphoproteins. Proteomics 2005; 5:4684-8. [PMID: 16267815 DOI: 10.1002/pmic.200500021] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pro-Q Diamond (Pro-Q DPS) is a commercially available stain that binds the phosphate moiety of phosphoproteins with high sensitivity and linearity. To conserve consumable costs we demonstrate that threefold diluted Pro-Q DPS offers the same sensitivity and linearity of signal to that obtained with undiluted Pro-Q DPS. The optimal conditions for Pro-Q DPS indicate that fixation, staining, and destaining of gels longer than 1 h, 2 h, and four 30-min incubations, respectively, are not required. The fixation and destaining solutions, but not the threefold diluted Pro-Q DPS, can be re-used without compromising the signal intensity or linear dynamic range. This modified protocol of Pro-Q DPS reduces the cost at least by fourfold, making the stain economically attractive for large-scale analysis of phosphoproteins.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Biochemistry Department, University of Missouri-Columbia, 109 Life Sciences Center, Columbia, MO 65211, USA
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214
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Zhan X, Desiderio DM. Comparative proteomics analysis of human pituitary adenomas: current status and future perspectives. MASS SPECTROMETRY REVIEWS 2005; 24:783-813. [PMID: 15495141 DOI: 10.1002/mas.20039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article will review the published research on the elucidation of the mechanisms of pituitary adenoma formation. Mass spectrometry (MS) plays a key role in those studies. Comparative proteomics has been used with the long-term goal to locate, detect, and characterize the differentially expressed proteins (DEPs) in human pituitary adenomas; to identify tumor-related and -specific biomarkers; and to clarify the basic molecular mechanisms of pituitary adenoma formation. The methodology used for comparative proteomics, the current status of human pituitary proteomics studies, and future perspectives are reviewed. The methodologies that are used in comparative proteomics studies of human pituitary adenomas are readily exportable to other different areas of cancer research.
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Affiliation(s)
- Xianquan Zhan
- Charles B. Stout Neuroscience Mass Spectrometry Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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215
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Abstract
Presently, phosphorylation of proteins is the most studied and best understood PTM. However, the analysis of phosphoproteins and phosphopeptides is still one of the most challenging tasks in contemporary proteome research. Since not every phosphoprotein is accessible by a certain method and identification of the phosphorylated amino acid residue is required in the majority of cases, various strategies for the detection and localization of phosphorylations have been developed. Identification and localization of protein phosphorylations is mostly done by MS nowadays but phosphoproteins and -peptides are often suppressed in comparison to the unphosphorylated species if measured in complex mixtures. Thus, the isolation of pure phosphopeptide samples is a main task. This review gives an overview over the most frequently used methods in isolation and detection of phosphoproteins and -peptides such as specific enrichment or separation strategies as well as the localization of the phosphorylated residues by various mass spectrometric techniques.
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Affiliation(s)
- Joerg Reinders
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany
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216
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Fujii K, Kondo T, Yokoo H, Yamada T, Matsuno Y, Iwatsuki K, Hirohashi S. Protein expression pattern distinguishes different lymphoid neoplasms. Proteomics 2005; 5:4274-86. [PMID: 16206328 DOI: 10.1002/pmic.200401286] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To identify proteins associated with the histological subtypes of lymphoid neoplasms, we studied the proteomes of 42 cell lines from human lymphoid neoplasms including Hodgkin's lymphoma (HL; four cell lines), B cell malignancies (19 cell lines), T cell malignancies (16 cell lines), and natural killer (NK) cell lymphoma (three cell lines). The protein spots were sequentially selected by (i) Wilcoxon or Kruskal-Wallis tests to find the spots whose intensity was significantly (p <0.05) different among the cell line groups, (ii) by statistical-learning methods to prioritize the spots according to their contribution to the classification, and (iii) by unsupervised classification methods to validate the classification robustness by the selected spots. The selected spots discriminated (i) between HL cells and other cells, (ii) between the cells from B cell malignancies, T cell malignancies, and NK cell lymphoma cells, and (iii) between HL cells and anaplastic large cell lymphoma cells. Among the 31 informative protein spots, MS identified 24 proteins corresponding to 23 spots. Previous reports did not correlate these proteins to lymphocyte differentiation, suggesting that a proteomic study would identify the novel mechanisms responsible for the histogenesis of lymphoid neoplasms. These proteins may have potential as differential diagnostic markers for lymphoid neoplasms.
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MESH Headings
- Amino Acid Sequence
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Diagnosis, Differential
- Electrophoresis, Gel, Two-Dimensional
- Hodgkin Disease/diagnosis
- Hodgkin Disease/metabolism
- Humans
- Killer Cells, Natural/metabolism
- Lymphoma/diagnosis
- Lymphoma/metabolism
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/metabolism
- Lymphoma, Non-Hodgkin/diagnosis
- Lymphoma, Non-Hodgkin/metabolism
- Lymphoma, T-Cell/diagnosis
- Lymphoma, T-Cell/metabolism
- Molecular Sequence Data
- Multivariate Analysis
- Proteome/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Kazuyasu Fujii
- Cancer Proteomics Project, National Cancer Center Research Institute, Tokyo, Japan
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217
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Loiselle DR, Thelin WR, Parker CE, Dicheva NN, Kesner BA, Mocanu V, Wang F, Milgram SL, Warren MRE, Borchers CH. Improved protein identification through the use of unstained gels. J Proteome Res 2005; 4:992-7. [PMID: 15952747 DOI: 10.1021/pr049785o] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, a method for improved protein identification of low-abundance proteins using unstained gels, in combination with robotics and matrix-assisted laser desorption/ionization tandem mass spectrometry, has been developed and evaluated. Omitting the silver-staining process resulted in increased protein identification scores, an increase in the number of peptides observed in the MALDI mass spectrum, and improved quality of the tandem mass spectrometry data.
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Affiliation(s)
- David R Loiselle
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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218
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Scrivener E, Boghigian BA, Golenko E, Bogdanova A, Jackson P, Mikulskis A, Denoyer E, Courtney P, Lopez MF, Patton WF. Performance validation of an improved Xenon-arc lamp-based CCD camera system for multispectral imaging in proteomics. Proteomics 2005; 5:4354-66. [PMID: 16206330 DOI: 10.1002/pmic.200500062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Advances in gel-based nonradioactive protein expression and PTM detection using fluorophores has served as the impetus for developing analytical instrumentation with improved imaging capabilities. We describe a CCD camera-based imaging instrument, equipped with both a high-pressure Xenon arc lamp and a UV transilluminator, which provides broad-band wavelength coverage (380-700 nm and UV). With six-position filter wheels, both excitation and emission wavelengths may be selected, providing optimal measurement and quantitation of virtually any dye and allowing excellent spectral resolution among different fluorophores. While spatial resolution of conventional fixed CCD camera imaging systems is typically inferior to laser scanners, this problem is circumvented with the new instrument by mechanically scanning the CCD camera over the sample and collecting multiple images that are subsequently automatically reconstructed into a complete high-resolution image. By acquiring images in succession, as many as four different fluorophores may be evaluated from a gel. The imaging platform is suitable for analysis of the wide range of dyes and tags commonly encountered in proteomics investigations. The instrument is unique in its capabilities of scanning large areas at high resolution and providing accurate selectable illumination over the UV/visible spectral range, thus maximizing the efficiency of dye multiplexing protocols.
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219
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Gillespie AS, Elliott E. Comparative advantages of imidazole–sodium dodecyl sulfate–zinc reverse staining in polyacrylamide gels. Anal Biochem 2005; 345:158-60. [PMID: 16125125 DOI: 10.1016/j.ab.2005.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Revised: 06/02/2005] [Accepted: 06/06/2005] [Indexed: 11/28/2022]
Affiliation(s)
- Amanda S Gillespie
- School of Biochemistry, Genetics, Microbiology and Plant Pathology, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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220
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Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics. Proteomics 2005; 5:1242-9. [PMID: 15732138 DOI: 10.1002/pmic.200401003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although two-dimensional gel electrophoresis (2-DE) has long been a favorite experimental method to screen proteomes, its reproducibility is seldom analyzed with the assistance of quantitative error models. The lack of models of residual distributions that can be used to assign likelihood to differential expression reflects the difficulty in tackling the combined effect of variability in spot intensity and uncertain recognition of the same spot in different gels. In this report we have analyzed a series of four triplicate two-dimensional gels of chicken embryo heart samples at two distinct development stages to produce such a model of residual distribution. In order to achieve this reference error model, a nonparametric procedure for consistent spot intensity normalization had to be established, and is also reported here. In addition to variability in normalized intensity due to various sources, the residual variation between replicates was observed to be compounded by failure to identify the spot itself (gel alignment). The mixed effect is reflected by variably skewed bimodal density distributions of residuals. The extraction of a global error model that accommodated such distribution was achieved empirically by machine learning, specifically by bootstrapped artificial neural networks. The model described is being used to assign confidence values to observed variations in arbitrary 2-DE gels in order to quantify the degree of over-expression and under-expression of protein spots.
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221
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Affiliation(s)
- Jonathan E Katz
- Louis Warschaw Prostate Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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222
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Shankar R, Gude N, Cullinane F, Brennecke S, Purcell AW, Moses EK. An emerging role for comprehensive proteome analysis in human pregnancy research. Reproduction 2005; 129:685-96. [PMID: 15923384 DOI: 10.1530/rep.1.00524] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Elucidation of underlying cellular and molecular mechanisms is pivotal to the comprehension of biological systems. The successful progression of processes such as pregnancy and parturition depends on the complex interactions between numerous biological molecules especially within the uterine microenvironment. The tissue- and stage-specific expression of these bio-molecules is intricately linked to and modulated by several endogenous and exogenous factors. Malfunctions may manifest as pregnancy disorders such as preterm labour, pre-eclampsia and fetal growth restriction that are major contributors to maternal and perinatal morbidity and mortality. Despite the immense amount of information available, our understanding of several aspects of these physiological processes remains incomplete. This translates into significant difficulties in the timely diagnosis and effective treatment of pregnancy-related complications. However, the emergence of powerful mass spectrometry-based proteomic techniques capable of identifying and characterizing multiple proteins simultaneously has added a new dimension to the field of biomedical research. Application of these high throughput methodologies with more conventional techniques in pregnancy-related research has begun to provide a novel perspective on the biochemical blueprint of pregnancy and its related disorders. Further, by enabling the identification of proteins specific to a disease process, proteomics is likely to contribute, not only to the comprehension of the underlying pathophysiologies, but also to the clinical diagnosis of multifactorial pregnancy disorders. Although the application of this technology to pregnancy research is in its infancy, characterization of the cellular proteome, unearthing of functional networks and the identification of disease biomarkers can be expected to significantly improve maternal healthcare in the future.
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Affiliation(s)
- Renu Shankar
- Department of Obstetrics and Gynaecology, The University of Melbourne, Melbourne, Australia.
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223
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Hauck SM, Schoeffmann S, Deeg CA, Gloeckner CJ, Swiatek-de Lange M, Ueffing M. Proteomic analysis of the porcine interphotoreceptor matrix. Proteomics 2005; 5:3623-36. [PMID: 16127731 DOI: 10.1002/pmic.200401223] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The interphotoreceptor matrix (IPM) is located between photoreceptors and pigment epithelium in the retina and is involved in fundamental functions of the visual cycle. These include visual pigment chromophore exchange, retinal adhesion, metabolite trafficking, and growth factor presentation. In general, IPM preparations are contaminated with intracellular proteins, as has also been described for other body fluids. This study aimed at identifying new components of the IPM by discriminating between truly secreted proteins and proteins that are part of the IPM for secondary reasons. "Soluble" porcine IPM was extracted from retina and pigment epithelium with PBS by two different procedures, followed by extraction with water alone that released "insoluble" IPM matrix sheets. Samples from all preparations were separated by 2-DE and a total of 140 protein spots were identified by MALDI-TOF and/or CapLC Q-TOF MS. Although identified proteins included several already known in the IPM, the majority had not been previously described in this structure. Gene ontology classifications allocated the identified proteins into nine different functional networks. The IPM preparations also included intracellular proteins from cells adjacent to the IPM, which may have resulted from cell disruption. This underlines the experimental difficulties of a biochemical analysis of the IPM as an intact compartment. We show here a strategy for predicting the probability of identified IPM proteins occurring in vivo by combined high-resolution protein separation methods with computational prediction methods. Thus, a set of potentially neuroprotective proteins could be extracted, including PEA-15, peroxiredoxin 5, alpha-B-crystallin, macrophage migration inhibitory factor, 78 kDa glucose-regulated protein (GRP78), protein disulfide-isomerase, and PEP-19, which have not been previously associated with the IPM. Furthermore, with immunohistochemical staining we could confirm the localization of GRP78 in the IPM on porcine eye sections, thus validating the proposed prediction method.
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Affiliation(s)
- Stefanie M Hauck
- GSF-National Research Centre for Environment and Health, Institute of Human Genetics, Neuherberg, Germany
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224
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Ottens AK, Kobeissy FH, Wolper RA, Haskins WE, Hayes RL, Denslow ND, Wang KKW. A Multidimensional Differential Proteomic Platform Using Dual-Phase Ion-Exchange Chromatography−Polyacrylamide Gel Electrophoresis/Reversed-Phase Liquid Chromatography Tandem Mass Spectrometry. Anal Chem 2005; 77:4836-45. [PMID: 16053296 DOI: 10.1021/ac050478r] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differential proteomic analysis has arisen as a large-scale means to discern proteome-wide changes upon treatment, injury, or disease. Tandem protein separation methods are required for large-scale differential proteomic analysis. Here, a novel multidimensional platform for resolving and differentially analyzing complex biological samples is presented. The platform, collectively termed CAX-PAGE/RPLC-MSMS, combines biphasic ion-exchange chromatography with polyacrylamide gel electrophoresis for protein separation, quantification, and differential band targeting, followed by capillary reversed-phase liquid chromatography and data-dependent tandem mass spectrometry for quantitative and qualitative peptide analysis. CAX-PAGE provides high protein resolving power with a theoretical peak capacity of 3570, extendable to 7600, a wide protein mass range verified from 16 to 273 kDa, and reproducible differential sample comparison without the added expense of fluorescent dyes and imaging equipment. Demonstrated using a neuroproteomic model, CAX-PAGE revealed an increased number of differential proteins, 137, compared with 82 found by 2D difference gel electrophoresis. When combined with RPLC-MSMS for protein identification, an additional quantification step is performed for internal validation, confirming a 2-fold or greater change in 89% of identified differential targets.
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Affiliation(s)
- Andrew K Ottens
- Center for Neuroproteomics and Biomarker Research, University of Florida, Gainesville, Florida 32610, USA.
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225
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Byon HR, Hong BJ, Gho YS, Park JW, Choi HC. Pseudo 3D Single-Walled Carbon Nanotube Film for BSA-Free Protein Chips. Chembiochem 2005; 6:1331-4. [PMID: 15997463 DOI: 10.1002/cbic.200500081] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hye Ryung Byon
- Department of Chemistry, Pohang University of Science and Technology, Hyoja-Dong, Pohang, Korea
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226
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Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B. Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. CURRENT PROTOCOLS IN BIOINFORMATICS 2005; Chapter 13:Unit 13.1. [PMID: 18428746 PMCID: PMC3863626 DOI: 10.1002/0471250953.bi1301s10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein-profiling technologies are reviewed, along with the accompanying data-analysis tools.
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227
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Faber MJ, Dalinghaus M, Lankhuizen IM, Bezstarosti K, Dekkers DHW, Duncker DJ, Helbing WA, Lamers JMJ. Proteomic changes in the pressure overloaded right ventricle after 6 weeks in young rats: Correlations with the degree of hypertrophy. Proteomics 2005; 5:2519-30. [PMID: 15912512 DOI: 10.1002/pmic.200401313] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Right ventricular (RV) hypertrophy is an important problem in congenital heart disease. We determined the alterations in phenotype that occur in the initial phase of RV hypertrophy and their possible correlations with the degree of hypertrophy. Therefore, we performed a differential proteomic profiling study on RV hypertrophy using an animal model of pulmonary artery banding (PAB) in parallel with hemodynamic characterization. The RV homogenates were subfractionated in myofilament and cytoplasmic proteins, which subsequently were separated by two-dimensional gel electrophoresis (2-DE), excised, and analyzed by mass spectrometry (MS). The cytoplasmic fraction showed expression changes in metabolic proteins, indicative of a shift from fatty acid to glucose as a substrate for energy supply. Up-regulation of three HSP-27s (1.9-, 1.7-, and 3.5-fold) indicated an altered stress response in RV hypertrophy. Detailed analysis by immunoblotting and MS showed that two of these HSP-27s were at least phosphorylated on Ser15. The myofilament fraction showed up-regulation of desmin and alpha-B-crystallin (1.4-and 1.3-fold, respectively). This alteration in desmin was confirmed by 1-DE immunoblots. Certain differentially expressed proteins, such as HSP-27, showed a significant correlation with the RV weight to the body weight ratio in the PAB rats, suggesting an association with the degree of hypertrophy.
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Affiliation(s)
- Matthijs J Faber
- Department of Pediatrics, Division of Pediatric Cardiology, Erasmus MC-Sophia Children's Hospital, Cardiovascular Research School COEUR, Erasmus University Medical Center, Rotterdam, The Netherlands
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228
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Kuruma H, Egawa S, Oh-Ishi M, Kodera Y, Maeda T. Proteome analysis of prostate cancer. Prostate Cancer Prostatic Dis 2005; 8:14-21. [PMID: 15477873 DOI: 10.1038/sj.pcan.4500764] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this paper, we briefly review cancer proteomics in general, with particular attention to our proteome analyses of prostate cancer. Our efforts include development of new tools and novel approaches to discovering proteins potentially useful as cancer diagnostic and/or prognostic biomarkers or as therapeutic targets. To this end, we analyzed prostate cancer proteomes using two-dimensional gel electrophoresis employing agarose gels for the initial isoelectric focusing step (agarose 2-DE), with mass spectrometry used for protein identification. Agarose 2-DE offers advantages over the more widely used immobilized pH gradient 2-DE for separating high molecular mass proteins (15-500 kDa), thereby increasing its power to detect changes in the cancer's high-molecular mass proteomes.
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Affiliation(s)
- H Kuruma
- Department of Urology, Kitasato University School of Medicine, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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229
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Serrano SMT, Shannon JD, Wang D, Camargo ACM, Fox JW. A multifaceted analysis of viperid snake venoms by two-dimensional gel electrophoresis: an approach to understanding venom proteomics. Proteomics 2005; 5:501-10. [PMID: 15627971 DOI: 10.1002/pmic.200400931] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complexity of Viperid venoms has long been appreciated by investigators in the fields of toxinology and medicine. However, it is only recently that the depth of that complexity has become somewhat quantitatively and qualitatively appreciated. With the resurgence of two-dimensional gel electrophoresis (2-DE) and the advances in mass spectrometry virtually all venom components can be visualized and identified given sufficient effort and resources. Here we present the use of 2-DE for examining venom complexity as well as demonstrating interesting approaches to selectively delineate subpopulations of venom proteins based on particular characteristics of the proteins such as antibody cross-reactivity or enzymatic activities. 2-DE comparisons between venoms from different species of the same genus (Bothrops) of snake clearly demonstrated both the similarity as well as the apparent diversity among these venoms. Using liquid chromatography/tandem mass spectrometry we were able to identify regions of the two-dimensional gels from each venom in which certain classes of proteins were found. 2-DE was also used to compare venoms from Crotalus atrox and Bothrops jararaca. For these venoms a variety of staining/detection protocols was utilized to compare and contrast the venoms. Specifically, we used various stains to visualize subpopulations of the venom proteomes of these snakes, including Coomassie, Silver, Sypro Ruby and Pro-Q-Emerald. Using specific antibodies in Western blot analyses of 2-DE of the venoms we have examined subpopulations of proteins in these venoms including the serine proteinase proteome, the metalloproteinase proteome, and the phospholipases A2 proteome. A functional assessment of the gelatinolytic activity of these venoms was also performed by zymography. These approaches have given rise to a more thorough understanding of venom complexity and the toxins comprising these venoms and provide insights to investigators who wish to focus on these venom subpopulations of proteins in future studies.
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Affiliation(s)
- Solange M T Serrano
- Laboratório Especial de Toxinologia Aplicada, CAT-CEPID, Instituto Butantan, Sao Paulo-SP, Brazil.
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230
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Kleiner O, Price DA, Ossetrova N, Osetrov S, Volkovitsky P, Drukier AK, Godovac-Zimmermann J. Ultra-high sensitivity multi-photon detection imaging in proteomics analyses. Proteomics 2005; 5:2322-30. [PMID: 15880791 DOI: 10.1002/pmic.200401271] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report on the use of 125I and 131I labeling and of new, multicolor, multi-photon detection (MPD) methods to routinely and quantitatively detect protein spots on two-dimensional gel electrophoresis plates in the zeptomole to attomole range. We demonstrate that the MPD methodology can be used to detect radioactive labels on two-dimensional gels and has several characteristics that are advantageous for functional proteomics. First, by using single particle detectors, the sensitivity for detection of radiolabels can be improved dramatically. Second, because single particle detectors can differentiate the particle energies produced by different decay processes, it is possible to choose combinations of radioisotopes that can be detected and quantified individually on the same 2-D gel. Third, the MPD technology is essentially linear over six to seven orders of magnitude, i.e., it is possible to accurately quantify radiolabeled proteins over a range from at least 60 zeptomoles to 60 femtomoles. Finally for radionuclides that decay by electron capture, e.g., with emission of both beta and gamma rays, co-incident detection of two particles/photons can be used to detect such radionuclides well below background radiation levels. These methods are used to monitor acidic/phosphorylated proteins in as little as 60 ng of HeLa cells proteins.
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Affiliation(s)
- Oliver Kleiner
- Department of Medicine, Centre for Molecular Medicine, University College London, London, UK
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231
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Witkamp RF. Genomics and systems biology - how relevant are the developments to veterinary pharmacology, toxicology and therapeutics? J Vet Pharmacol Ther 2005; 28:235-45. [PMID: 15953196 DOI: 10.1111/j.1365-2885.2005.00662.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This review discusses some of the recent developments in genomics and its current and future relevance for veterinary pharmacology and toxicology. With the rapid progress made in this field several new approaches in pharmacological and toxicological research have developed and drug discovery and drug development strategies have changed dramatically. In this review, the term genomics is used to encompass the three sub-disciplines transcriptomics, proteomics and metabolomics (or metabonomics) to describe the formation and fate of mRNA, proteins and metabolites, respectively. The current status and methods of the technology and some applications are briefly described. Although the DNA sequencing programmes are receiving considerable attention, the real value of genomics for pharmacology and toxicology is brought by the parallel developments in bio-informatics, bio-statistics and the integration of biology with mathematics and information technology. The ultimate level of integration is now mostly called systems biology, where mRNA, proteins and metabolites are being analysed in parallel, using a complete arsenal of analytical techniques (DNA-array, LC-MS/MS, GC-MS/MS, NMR, etc.). The information thus collected is analysed, integrated, linked to database information and translated to pathways and systems. This approach offers an enormous potential to study disease mechanisms and find new drug targets. Thus far, genomics and systems biology have not been introduced significantly in typical veterinary pharmacological and toxicological research programmes. The high costs and complexity connected to these large projects often form major obstacles for research groups with limited budgets. In other veterinary areas and disciplines, including infectious diseases, animal production and food-safety more examples of application are available. Genomics and bio-informatics provide outstanding opportunities to study pharmacology and toxicology in a more holistic way, taking into account the complexity of biological systems and based on the basic principles of physiology and the concept of homeostasis. Knowledge of biology, in vivo and in vitro models, and comparative pharmacology/toxicology is essential here, creating excellent opportunities for the veterinary trained scientist.
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232
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233
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Abstract
Proteomics is a fast-growing discipline in biomedicine that can be defined as the large-scale characterization of the entire protein complement of a cell, tissue or organism. Because protein levels and function may be critically dependent upon post-transcriptional mechanisms (e.g. post-translational modifications), there has been significant interest in directly examining protein structure and function. It is now clear that proteomics studies may unmask previously unknown functions of proteins or protein interactions. However, proteomics in the field of rheumatology is still in its infancy. This review guides the reader through the consecutive steps of a proteomics study and provides an outline of the applications in the field of rheumatology, which may range from proteome analyses of biological fluids of rheumatic diseases to identify possible new diagnostic tools, towards more pathophysiological studies on target tissues, such as synovial tissue or articular cartilage. Proteomics has great potential in the field of rheumatology and will no doubt have a great impact on our molecular understanding of these complex diseases.
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Affiliation(s)
- K Tilleman
- Laboratory for Molecular Immunology and Inflammation, Division of Rheumatology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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234
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Zhao C, Wang J, Cao M, Zhao K, Shao J, Lei T, Yin J, Hill GG, Xu N, Liu S. Proteomic changes in rice leaves during development of field-grown rice plants. Proteomics 2005; 5:961-72. [PMID: 15712239 DOI: 10.1002/pmic.200401131] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Of the numerous factors affecting rice yield, how solar radiation is transformed into biomass through rice leaves is the most important. We have analyzed proteomic changes in rice leaves collected from six different developing stages (vegetative to ripening). We studied protein expression profiles of rice leaves by running two-dimensional gel electrophoresis. Differential protein expression among the six phases were analyzed by image analysis, which allowed the identification of 49 significantly different gel spots. The spots were further verified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, in which 89.8% of them were confirmed to be rice proteins. Finally, we confirmed some of the interesting rice proteins by immunoblotting. Three major conclusions can be drawn from these experimental results. (i) Protein expression in rice leaves, at least for high or middle abundance proteins, is attenuated during growth (especially some chloroplast proteins). However, the change is slow and the expression profiles are relatively stable during rice development. (ii) Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), a major protein in rice leaves, is expressed at constant levels at different growth stages. Interestingly, a high ratio of degradation of the RuBisCO large subunit was found in all samples. This was confirmed by two approaches, mass spectrometry and immunoblotting. The degraded fragments are similar to other digested products of RuBisCO mediated by free radials. (iii) The expression of antioxidant proteins such as superoxide dismutase and peroxidase decline at the early ripening stage.
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Affiliation(s)
- Caifeng Zhao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
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235
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Nishimura T, Ogiwara A, Fujii K, Kawakami T, Kawamura T, Anyouji H, Kato H. Disease proteomics toward bedside reality. J Gastroenterol 2005; 40 Suppl 16:7-13. [PMID: 15902957 DOI: 10.1007/bf02990572] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The human genome has been sequenced, and investigation of its products has become possible in a sequence-based framework. More than 200,000 protein species are expressed in the body from approximately 30000 human genes. The term proteome, coined as a linguistic equivalent to the concept of genome, is used to describe the complete set of proteins that is expressed, and modified following expression, by the entire genome in a cell at any one time. Protein types and amounts expressed in a body vary greatly depending upon whether it is healthy or ill. Therefore, proteomics is attracting an increasing interest in its application to better understanding of disease processes, to development of new biomarkers for diagnosis and early detection of disease, and to accelerate drug development. There are numerous opportunities for medicine, although it is quite challenging to meet the needs for high sensitivity and high throughput required for disease-related investigations.
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Affiliation(s)
- Toshihide Nishimura
- Clinical Proteome Center, Tokyo Medical University, 2-6-1 Nishi-shinjuku Shinjuku-ku, Tokyo 163-0217, Japan
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236
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237
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Park YC, Lee DY, Lee DH, Kim HJ, Ryu YW, Seo JH. Proteomics and physiology of erythritol-producing strains. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815:251-60. [PMID: 15652814 DOI: 10.1016/j.jchromb.2004.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 10/22/2004] [Indexed: 11/29/2022]
Abstract
In-depth knowledge bases on physiological properties of microbes are required to design a better microbial system at a gene level and to develop an industrially viable process in an optimized scheme. Proteomic analyses of industrially useful microorganisms are particularly important for achieving such objectives. In this review, industrial application of erythritol in food and pharmaceutical areas and proteomic techniques for erythritol-producing microbes were presented. Proteomic technologies for erythritol-producing strains such as Candida magnoliae contained protein or peptide sample preparation for two-dimensional electrophoresis and mass spectrometry, analysis of proteome with matrix assisted laser desorption-ionization/time-of-flight mass spectrometry, liquid chromatography/electrospray ionization/tandem mass spectrometry and similarity searching algorithms. The proteomic information was applied to predict the carbon metabolism of erythritol-synthesizing microorganisms.
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Affiliation(s)
- Yong-Cheol Park
- School of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul 151-742, Korea
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238
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Chakravarti B, Gallagher SR, Chakravarti DN. Difference Gel Electrophoresis (DIGE) Using CyDye DIGE Fluor Minimal Dyes. ACTA ACUST UNITED AC 2005; Chapter 10:Unit 10.23. [DOI: 10.1002/0471142727.mb1023s69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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239
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Paulson L, Persson R, Karlsson G, Silberring J, Bierczynska-Krzysik A, Ekman R, Westman-Brinkmalm A. Proteomics and peptidomics in neuroscience. Experience of capabilities and limitations in a neurochemical laboratory. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:202-213. [PMID: 15706622 DOI: 10.1002/jms.740] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The increasing use of proteomics has created a basis for new strategies to develop methodologies for rapid identification of protein patterns in living organisms. It has also become evident that proteomics has other potential applications than protein and peptide identification, e.g. protein characterization, with the aim of revealing their structure, function(s) and interactions of proteins. In comparative proteomics studies, the protein expression of a certain biological system is compared with another system or the same system under perturbed conditions. Global identification of proteins in neuroscience is extremely complex, owing to the limited availability of biological material and very low concentrations of the molecules. Moreover, in addition to proteins, there are number of peptides that must also be considered in global studies on the central nervous system. In this overview, we focus on and discuss problems related to the different sources of biological material and sample handling, which are part of all preparatory and analytical steps. Straightforward protocols are desirable to avoid excessive purification steps, since loss of material at each step is inevitable. We would like to merge the two worlds of proteomics/peptidomics and neuroscience, and finally we consider different practical and technical aspects, illustrated with examples from our laboratory.
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Affiliation(s)
- Linda Paulson
- Institute of Clinical Neuroscience, Experimental Neuroscience Section, The Sahlgrenska Academy at Göteborg University, 431 80 Mölndal, Sweden
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240
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Chapter 5 Phosphorylation-specific analysis strategies for mass spectrometry: enhanced detection of phosphorylated proteins and peptides. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0166-526x(05)46005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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241
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Oberemm A, Meckert C, Brandenburger L, Herzig A, Lindner Y, Kalenberg K, Krause E, Ittrich C, Kopp-Schneider A, Stahlmann R, Richter-Reichhelm HB, Gundert-Remy U. Differential signatures of protein expression in marmoset liver and thymus induced by single-dose TCDD treatment. Toxicology 2005; 206:33-48. [PMID: 15590107 DOI: 10.1016/j.tox.2004.06.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Revised: 06/18/2004] [Accepted: 06/21/2004] [Indexed: 12/30/2022]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an ubiquitously distributed environmental pollutant. Health effects have been studied intensively, but low-dose effects are quite complex and not yet fully understood. In many studies, the immune system was identified as the most sensitive target. Here, we demonstrate changes of protein expression in liver and thymus of male marmosets (Callithrix jacchus) which were subjected to a single dose of a subcutaneous injection of 100 ng/kg body weight TCDD. Histopathological examination revealed myocardial fibrosis, but there were no significant findings in pathology and histopathology of liver and thymus. In order to detect more subtle treatment-related changes, we performed a comparative proteomic investigation of liver and thymus using a 2-D gel electrophoresis based proteomics approach. Fluorescence labeling and automated image analysis was used to enhance sensitivity and reproducibility. In both organs, distinct changes of protein expression were detected which were more pronounced in thymus, where the pattern of deregulated proteins could be clearly related to immune responses. In the thymus of treated animals, several toxicologically relevant factors were increased, including chaperones, glycerol-3-phosphate dehydrogenase, and adseverin. Among others, vimentin, Ca-dependent protease and protein disulfide isomerase were downregulated. In the liver, transferrins, lamin A and HSP70 were upregulated, whereas thymidine phosphorylase (synonyms: endothelial cell growth factor, PD-ECGF, gliostatin) was significantly reduced. Comparative analysis of deregulated proteins in both organs revealed a pattern of related functions, which fits well into the existing knowledge of the toxic processes and mechanisms underlying TCDD-mediated toxicity.
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Affiliation(s)
- Axel Oberemm
- Federal Institute for Risk Assessment, Thielallee 88-92, 14195 Berlin, Germany.
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242
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Ibuki Y, Naitou H, Ohashi N, Goto R. Proteome Analysis of UV-B–Induced Anti-apoptotic Regulatory Factors¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-09-01-ra-297r1.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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243
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Wu J, Lenchik NJ, Pabst MJ, Solomon SS, Shull J, Gerling IC. Functional characterization of two-dimensional gel-separated proteins using sequential staining. Electrophoresis 2005; 26:225-37. [PMID: 15624177 DOI: 10.1002/elps.200406176] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Proteins separated by two-dimensional (2-D) gel electrophoresis can be visualized using various protein staining methods. This is followed by downstream procedures, such as image analysis, gel spot cutting, protein digestion, and mass spectrometry (MS), to characterize protein expression profiles within cells, tissues, organisms, or body fluids. Characterizing specific post-translational modifications on proteins using MS of peptide fragments is difficult and labor-intensive. Recently, specific staining methods have been developed and merged into the 2-D gel platform so that not only general protein patterns but also patterns of phosphorylated and glycosylated proteins can be obtained. We used the new Pro-Q Diamond phosphoprotein dye technology for the fluorescent detection of phosphoproteins directly in 2-D gels of mouse leukocyte proteins, and Pro-Q Emerald 488 glycoprotein dye to detect glycoproteins. These two fluorescent stains are compatible with general protein stains, such as SYPRO Ruby stain. We devised a sequential procedure using Pro-Q Diamond (phosphoprotein), followed by Pro-Q Emerald 488 (glycoprotein), followed by SYPRO Ruby stain (general protein stain), and finally silver stain for total protein profile. This multiple staining of the proteins in a single gel provided parallel determination of protein expression and preliminary characterization of post-translational modifications of proteins in individual spots on 2-D gels. Although this method does not provide the same degree of certainty as traditional MS methods of characterizing post-translational modifications, it is much simpler, faster, and does not require sophisticated equipment and expertise in MS.
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Affiliation(s)
- Jian Wu
- Department of Medicine, University of Tennessee,Health Science Center, Memphis, TN 38104, USA
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Roque ACA, Lowe CR. Lessons from nature: On the molecular recognition elements of the phosphoprotein binding-domains. Biotechnol Bioeng 2005; 91:546-55. [PMID: 15959902 DOI: 10.1002/bit.20561] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The reversible phosphorylation of proteins regulates many biological processes. Despite the technological advances in the enrichment and detection of phosphorylated proteins, the currently available techniques still struggle with the complexity of the human proteome. The aim of this review is to highlight the molecular recognition elements of the interaction between phosphorylated proteins and peptides and pTyr or pSer/Thr-binding domains. The identification of the recognition features of the naturally occurring pTyr- and pSer/Thr-binding domains can contribute to an understanding of the molecular aspects of the affinity and specificity for phosphorylated residues. This might inspire the design of small "biomimetic" molecules with potential applications in assessing the extent of the phosphoproteome using affinity-based strategies.
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Affiliation(s)
- A Cecília A Roque
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom.
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245
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Kobi D, Zugmeyer S, Potier S, Jaquet-Gutfreund L. Two-dimensional protein map of an ?ale?-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res 2004; 5:213-30. [PMID: 15556083 DOI: 10.1016/j.femsyr.2004.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 06/28/2004] [Accepted: 07/01/2004] [Indexed: 11/28/2022] Open
Abstract
The first protein map of an ale-fermenting yeast is presented in this paper: 205 spots corresponding to 133 different proteins were identified. Comparison of the proteome of this ale strain with a lager brewing yeast and the Saccharomyces cerevisiae strain S288c confirmed that this ale strain is much closer to S288c than the lager strain at the proteome level. The dynamics of the ale-brewing yeast proteome during production-scale fermentation was analysed at the beginning and end of the first and the third usage of the yeast (called generation in the brewing industry). During the first generation, most changes were related to the switch from aerobic propagation to anaerobic fermentation. Fewer changes were observed during the third generation but certain stress-response proteins such as Hsp26p, Ssa4p and Pnc1p exhibited constitutive expression in subsequent generations. The ale brewing yeast strain appears to be quite well adapted to fermentation conditions and stresses.
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Affiliation(s)
- Dominique Kobi
- TEPRAL, Centre de recherche des brasseries Kronenbourg, 68 route d'Oberhausbergen, F-67037 Strasbourg Cedex, France
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246
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Hardy E, Castellanos-Serra LR. "Reverse-staining" of biomolecules in electrophoresis gels: analytical and micropreparative applications. Anal Biochem 2004; 328:1-13. [PMID: 15081901 DOI: 10.1016/j.ab.2004.02.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Negative or reverse staining using imidazole and zinc salts for protein detection in electrophoresis gels was originally introduced in 1990. The method is based on the selective precipitation of zinc imidazolate in the gel except in the zones where proteins are located. The method was later adapted to allow high-sensitivity negative detection of nucleic acids and bacterial lipopolysaccharides. It provides a practically quantitative recovery of intact biomolecules and is a method of choice for micropreparative applications of gel electrophoresis to proteomics and similar structural studies. Zinc-mediated protein fixation in the gel is fully reversible and the eluted biomolecules are neither chemically modified nor contaminated with organic dyes. Here we present a detailed compilation of practical methods for implementing these techniques with emphasis in their analytical or micropreparative applications.
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Affiliation(s)
- Eugenio Hardy
- Center for Genetic Engineering and Biotechnology, Division of Physical Chemistry, P.O. Box 6162, Havana City, Cuba
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248
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Abstract
Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the workhorse for proteomics. In spite of promising alternative or complementary technologies (e.g. multidimensional protein identification technology, stable isotope labelling, protein or antibody arrays) that have emerged recently, 2-DE is currently the only technique that can be routinely applied for parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. 2-DE enables the separation of complex mixtures of proteins according to isoelectric point (pI), molecular mass (Mr), solubility, and relative abundance. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms or post-translational modifications. This is in contrast to liquid chromatography-tandem mass spectrometry based methods, which perform analysis on peptides, where Mr and pI information is lost, and where stable isotope labelling is required for quantitative analysis. Today's 2-DE technology with IPGs (Görg et al., Electrophoresis 2000, 21, 1037-1053), has overcome the former limitations of carrier ampholyte based 2-DE (O'Farrell, J. Biol. Chem. 1975, 250, 4007-4021) with respect to reproducibility, handling, resolution, and separation of very acidic and/or basic proteins. The development of IPGs between pH 2.5-12 has enabled the analysis of very alkaline proteins and the construction of the corresponding databases. Narrow-overlapping IPGs provide increased resolution (delta pI = 0.001) and, in combination with prefractionation methods, the detection of low abundance proteins. Depending on the gel size and pH gradient used, 2-DE can resolve more than 5000 proteins simultaneously (approximately 2000 proteins routinely), and detect and quantify < 1 ng of protein per spot. In this article we describe the current 2-DE/MS workflow including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 2-DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two-dimensional protein databases.
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Affiliation(s)
- Angelika Görg
- Department of Proteomics, Technische Universität München, Freising-Weihenstephan, Germany.
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Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem 2004; 37:121-52. [PMID: 15376619 DOI: 10.1007/978-1-4757-5806-1_3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
This review focuses on how membrane lipid rafts have been detected and isolated, mostly from lymphocytes, and their associated proteins identified. These proteins include transmembrane antigens/receptors, GPI-anchored proteins, cytoskeletal proteins, Src-family protein kinases, G-proteins, and other proteins involved in signal transduction. To further understand the biology of lipid rafts, new methodological approaches are needed to help characterize the raft protein component, and changes that occur in this component as a result of cell perturbation. We describe the application of new proteomic approaches to the identification and quantification of raft proteins in T-lymphocytes. Similar approaches, applied to other model cell systems, will provide valuable new insights into both cellular signal transduction and lipid raft biology.
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250
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Suber RL, Flanders VL, Campa MJ, Patz EF. Accentuation of differentially expressed proteins using phage technology. Anal Biochem 2004; 333:351-7. [PMID: 15450812 DOI: 10.1016/j.ab.2004.06.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/18/2022]
Abstract
Protein profiling is frequently used to elucidate disease-specific or differentially expressed proteins. While recent developments have resulted in improved differential profiling, alternative expression platforms that complement existing techniques are continually being explored. We developed a novel method utilizing the amplification and selection capabilities of random peptide-expressing M13 bacteriophage to accentuate differentially expressed proteins in biologic specimens. While the current study used this method to demonstrate differentially expressed proteins in lung cancer tissue in comparison to normal lung tissue, this approach is applicable to a wide range of sample types.
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Affiliation(s)
- R Lee Suber
- Department of Radiology, Duke University Medical Center, Durham, NC, USA
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