1
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Woodland B, Necakov A, Coorssen JR. Optimized Proteome Reduction for Integrative Top–Down Proteomics. Proteomes 2023; 11:proteomes11010010. [PMID: 36976889 PMCID: PMC10059017 DOI: 10.3390/proteomes11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Integrative top–down proteomics is an analytical approach that fully addresses the breadth and complexity needed for effective and routine assessment of proteomes. Nonetheless, any such assessments also require a rigorous review of methodology to ensure the deepest possible quantitative proteome analyses. Here, we establish an optimized general protocol for proteome extracts to improve the reduction of proteoforms and, thus, resolution in 2DE. Dithiothreitol (DTT), tributylphosphine (TBP), and 2-hydroxyethyldisulfide (HED), combined and alone, were tested in one-dimensional SDS-PAGE (1DE), prior to implementation into a full 2DE protocol. Prior to sample rehydration, reduction with 100 mM DTT + 5 mM TBP yielded increased spot counts, total signal, and spot circularity (i.e., decreased streaking) compared to other conditions and reduction protocols reported in the literature. The data indicate that many widely implemented reduction protocols are significantly ‘under-powered’ in terms of proteoform reduction and thus, limit the quality and depth of routine top–down proteomic analyses.
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Affiliation(s)
- Breyer Woodland
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Aleksandar Necakov
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Ronin Institute, Montclair, NJ 07043, USA
- Correspondence:
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2
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Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) is an elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2D-GE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The use of an internal pooled standard makes 2D-DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. Technical limitations of this technique (i.e., underrating of low abundant, high molecular mass and integral membrane proteins) are counterbalanced by the incomparable separation power which allows proteoforms and unknown PTM (posttranslational modification) identification. Moreover, the image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.
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Affiliation(s)
- Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Segrate, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Segrate, Italy.
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3
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Lebedenko AA, Afonin AA, Semernik OE, Loginova IG, Gunko VO, Larichkin AV, Alliluyev IA, Galkina GA, Panova IV. Proteomic analysis of blood serum - a new approach to the search for diagnostic markers of bronchial asthma in children. Klin Lab Diagn 2022; 67:81-84. [PMID: 35192752 DOI: 10.51620/0869-2084-2022-67-2-81-84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Currently, bronchial asthma (BA) is one of the most pressing medical and social problems, the molecular aspects of the formation and development of BA are insufficiently studied and the diagnosis is not perfect. Carrying out proteomic analysis of BA will not only reveal new biomarkers specific to this disease, but also bring us closer to understanding its pathogenetic mechanisms. The purpose of the study: to study the proteomic profile of blood serum of children with BA to identify proteins associated with this disease A comprehensive clinical and laboratory examination of children suffering from BA and control group patients was performed. Proteomic analysis of depleted blood serum included high-resolution two-dimensional electrophoresis (1 direction: immobiline strips 17cm, pH 3-10, 2 direction: denaturing electrophoresis in 12.5% polyacrylamide gel), protein staining on gels with fluorescent dye Flamingo, protein identification by MALDI-TOF mass spectrometry using the search algorithm Mascot and the Swiss-Prot database. Comparison of the proteomic profile of BA serum and the control group patients serum allowed us to establish that the production of a number of proteins is reduced in this pathology. Among them, proteins in the molecular weight range of 16-33 kDa (p<0.05) were identified: glutathione peroxidase 3, transtyretin, complement components C4b and C3. Research shows that changes in the children's serum proteome occur in BA, affecting proteins that play an important role in immune responses, ligand transport, and antioxidant protection. Special attention should be paid to the differences identified in the course of this work (glutathione peroxidase, transtyretin, C3 and C4 fragments of the complement system) or their combinations. Studying the features of their expression will expand our understanding of the molecular mechanisms underlying chronic inflammation of this disease.
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4
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Asgarov R, Sen MK, Mikhael M, Karl T, Gyengesi E, Mahns DA, Malladi CS, Münch GW. Characterisation of the Mouse Cerebellar Proteome in the GFAP-IL6 Model of Chronic Neuroinflammation. THE CEREBELLUM 2021; 21:404-424. [PMID: 34324160 DOI: 10.1007/s12311-021-01303-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/14/2022]
Abstract
GFAP-IL6 transgenic mice are characterised by astroglial and microglial activation predominantly in the cerebellum, hallmarks of many neuroinflammatory conditions. However, information available regarding the proteome profile associated with IL-6 overexpression in the mouse brain is limited. This study investigated the cerebellum proteome using a top-down proteomics approach using 2-dimensional gel electrophoresis followed by liquid chromatography-coupled tandem mass spectrometry and correlated these data with motor deficits using the elevated beam walking and accelerod tests. In a detailed proteomic analysis, a total of 67 differentially expressed proteoforms including 47 cytosolic and 20 membrane-bound proteoforms were identified. Bioinformatics and literature mining analyses revealed that these proteins were associated with three distinct classes: metabolic and neurodegenerative processes as well as protein aggregation. The GFAP-IL6 mice exhibited impaired motor skills in the elevated beam walking test measured by their average scores of 'number of footslips' and 'time to traverse' values. Correlation of the proteoforms' expression levels with the motor test scores showed a significant positive correlation to peroxiredoxin-6 and negative correlation to alpha-internexin and mitochondrial cristae subunit Mic19. These findings suggest that the observed changes in the proteoform levels caused by IL-6 overexpression might contribute to the motor function deficits.
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Affiliation(s)
- Rustam Asgarov
- Pharmacology Unit, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Monokesh K Sen
- Proteomics and Lipidomics Lab, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Meena Mikhael
- Mass Spectrometry Facility, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Tim Karl
- Behavioural Neuroscience Lab, School of Medicine, Western Sydney University, Penrith, NSW, Australia.,Neuroscience Research Australia (NeuRA), Randwick, NSW, 2031, Australia.,School of Medical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Erika Gyengesi
- Pharmacology Unit, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - David A Mahns
- Integrative Physiology Lab, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Chandra S Malladi
- Proteomics and Lipidomics Lab, School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Gerald W Münch
- School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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5
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Refinement of two-dimensional electrophoresis for vitreous proteome profiling using an artificial neural network. Anal Bioanal Chem 2019; 411:5115-5126. [DOI: 10.1007/s00216-019-01887-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/18/2019] [Accepted: 04/30/2019] [Indexed: 01/07/2023]
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6
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Handtke S, Albrecht D, Otto A, Becher D, Hecker M, Voigt B. The Proteomic Response of Bacillus pumilus Cells to Glucose Starvation. Proteomics 2019; 18. [PMID: 29193752 DOI: 10.1002/pmic.201700109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 10/23/2017] [Indexed: 01/07/2023]
Abstract
Since starvation for carbon sources is a common condition for bacteria in nature and it can also occur in industrial fermentation processes due to mixing zones, knowledge about the response of cells to carbon starvation is beneficial. The preferred carbon source for bacilli is glucose. The response of Bacillus pumilus cells to glucose starvation using metabolic labeling and quantitative proteomics was analyzed. Glucose starvation led to an extensive reprogramming of the protein expression pattern in B. pumilus. The amounts of proteins of the central carbon metabolic pathways (glycolysis and TCC) remained stable in starving cells. Proteins for gluconeogenesis were found in higher amounts during starvation. Furthermore, many proteins involved in acquisition and usage of alternative carbon sources were present in elevated amounts in starving cells. Enzymes for fatty acid degradation and proteases and peptidases were also found in higher abundance when cells entered stationary phase. Among the proteins found in lower amounts were many enzymes involved in amino acid and nucleotide synthesis and several NRPS and PKS proteins.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany
| | - Andreas Otto
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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7
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Abstract
Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.
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Affiliation(s)
- Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via f.lli Cervi, 93, 20090, Segrate, Milan, Italy.
- U.O. Proteomica clinica, IRCCS Policlinico San Donato, 20097, San Donato, Milan, Italy.
- Istituto di Bioimmagini e Fisiologia Molecolare, CNR, 20090, Segrate, Milan, Italy.
| | - Daniele Capitanio
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via f.lli Cervi, 93, 20090, Segrate, Milan, Italy
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8
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Small RNA mediated repression of subtilisin production in Bacillus licheniformis. Sci Rep 2017; 7:5699. [PMID: 28720814 PMCID: PMC5516005 DOI: 10.1038/s41598-017-05628-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/31/2017] [Indexed: 01/08/2023] Open
Abstract
The species Bacillus licheniformis includes important strains that are used in industrial production processes. Currently the physiological model used to adapt these processes is based on the closely related model organism B. subtilis. In this study we found that both organisms reveal significant differences in the regulation of subtilisin, their main natural protease and a product of industrial fermentation processes. We identified and characterized a novel antisense sRNA AprAs, which represents an RNA based repressor of apr, the gene encoding for the industrial relevant subtilisin protease. Reduction of the AprAs level leads to an enhanced proteolytic activity and an increase of Apr protein expression in the mutant strain. A vector based complementation of the AprAs deficient mutant confirmed this effect and demonstrated the necessity of cis transcription for full efficiency. A comparative analysis of the corresponding genome loci from B. licheniformis and B. subtilis revealed the absence of an aprAs promoter in B. subtilis and indicates that AprAs is a B. licheniformis species specific phenomenon. The discovery of AprAs is of great biotechnological interest since subtilisin Carlsberg is one of the main products of industrial fermentation by B. licheniformis.
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9
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Handtke S, Albrecht D, Zühlke D, Otto A, Becher D, Schweder T, Riedel K, Hecker M, Voigt B. Bacillus pumilus KatX2 confers enhanced hydrogen peroxide resistance to a Bacillus subtilis PkatA::katX2 mutant strain. Microb Cell Fact 2017; 16:72. [PMID: 28446175 PMCID: PMC5406934 DOI: 10.1186/s12934-017-0684-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/19/2017] [Indexed: 11/27/2022] Open
Abstract
Background Bacillus pumilus cells exhibit a significantly higher resistance to hydrogen peroxide compared to closely related Bacilli like Bacillus subtilis. Results In this study we analyzed features of the catalase KatX2 of B. pumilus as one of the most important parts of the cellular response to hydrogen peroxide. KatX2, the vegetative catalase expressed in B. pumilus, was compared to the vegetative catalase KatA of B. subtilis. Data of our study demonstrate that B. pumilus can degrade toxic concentrations of hydrogen peroxide faster than B. subtilis. By replacing B. subtiliskatA gene by katX2 we could significantly enhance its resistance to H2O2 and its potential to eliminate this toxic compound. Mutant cells showed a 1.5- to 2-fold higher survival to toxic concentrations of hydrogen peroxide compared to wild type cells. Furthermore, we found reversible but also irreversible oxidations of the KatX2 protein which, in contrast to KatA, contains several cysteine residues. Conclusions Our study indicates that the catalase KatX2 plays a major role in the increased resistance of B. pumilus to oxidative stress caused by hydrogen peroxide. Resistance to hydrogen peroxide of other Bacilli can be enhanced by exchanging the native catalase in the cells with katX2. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0684-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Daniela Zühlke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Andreas Otto
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Kathrin Riedel
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany. .,Institute of Marine Biotechnology, 17489, Greifswald, Germany. .,Research Institute for Leather and Plastic Sheeting, Meißner-Ring 1-5, 09599, Freiberg, Germany.
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10
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Brown S, Norris G. Improved consistency in 2D gel electrophoresis: Sheep plasma as a test case. Electrophoresis 2016; 38:906-913. [PMID: 27925263 DOI: 10.1002/elps.201600433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/09/2022]
Abstract
Two-dimensional (2D) gel electrophoresis is a well-proven proteomic technique; however, sample-specific optimisation can often be necessary in order to get consistent quantitation. In particular, plasma samples are often smeared on 2D gels making spot matching difficult. A variety of different sample preparation and 2D methods were tested by using sheep plasma, and it was found that lowering sample pH prior to precipitation, using a long voltage gradient for isoelectric focusing and the inclusion of carrier ampholytes in the electrode wicks, improved both the quality and consistency of spot resolution. Analysis of the internal standards from two different DIGE experiments, one with conventional methodology and one with the improved method, showed that along with substantially improving the number of spots resolved, the average CV (coefficient of variation) of matched standards was lower with the new method. 428 matched spots were found using the improved method compared to 208 matched spots using conventional methodology. For the 174 spots that were matched between the two DIGE experiments, the average CV's of spot volumes were also significantly lower, at 0.20 for the new method compared to 0.24 for the conventional method (p < 0.001).
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Affiliation(s)
- Stuart Brown
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Gillian Norris
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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11
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Zwicker P, Schultze N, Niehs S, Methling K, Wurster M, Albrecht D, Bernhardt J, Wachlin G, Lalk M, Lindequist U, Haertel B. A proteomic approach for the identification of immunotoxic properties of Tulipalin A. Proteomics 2016; 16:2997-3008. [DOI: 10.1002/pmic.201600130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Paula Zwicker
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Nadin Schultze
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Sarah Niehs
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Karen Methling
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Martina Wurster
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dirk Albrecht
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Gerhild Wachlin
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Michael Lalk
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Ulrike Lindequist
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Beate Haertel
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
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12
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Arentz G, Weiland F, Oehler MK, Hoffmann P. State of the art of 2D DIGE. Proteomics Clin Appl 2015; 9:277-88. [DOI: 10.1002/prca.201400119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/13/2014] [Accepted: 11/10/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Georgia Arentz
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Florian Weiland
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Martin K. Oehler
- School of Paediatrics and Reproductive Health; Research Centre for Reproductive Health; Robinson Institute; University of Adelaide; SA Australia
- Department of Gynaecological Oncology; Royal Adelaide Hospital; Adelaide SA Australia
| | - Peter Hoffmann
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
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13
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Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach. J Biotechnol 2014; 192 Pt A:204-14. [PMID: 25281541 DOI: 10.1016/j.jbiotec.2014.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Sonja Volland
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Karen Methling
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Jenny Nehls
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428 Jülich, Germany.
| | | | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
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14
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Zhu H, Luo L, Hu S, Dong K, Li G, Zhang T. Treating Alzheimer's disease with Yizhijiannao granules by regulating expression of multiple proteins in temporal lobe. Neural Regen Res 2014; 9:1283-7. [PMID: 25221580 PMCID: PMC4160854 DOI: 10.4103/1673-5374.137575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 12/17/2022] Open
Abstract
Yizhijiannao granules have been shown to improve cognitive function in Alzheimer's disease patients. The present study sought to explore the mechanisms involved in the cognitive enhancing effects of Yizhijiannao granule. Senescence-accelerated mouse prone 8 mice with learning and memory disorders were intragastrically treated with Yizhijiannao granule for 8 weeks. Mice intragastrically treated with double distilled water for 8 weeks were considered as the control group. 2D gel electrophoresis was used to isolate total protein from the temporal lobe of senescence-accelerated mouse prone 8 mice, and differential protein spots were obtained by mass spectrometry. Thirty-seven differential protein spots were found in the temporal lobe area of both groups. Ten protein spots were identified: high mobility group box 1, dimethylarginine dimethylaminohydrolase-1, neuroglobin, hemoglobin beta adult major chain, peroxiredoxin-6, cofilin-1, flotillin 1, peptidylprolyl isomerase A, voltage-dependent anion channel-2 and chaperonin containing TCP1, and subunit 2. Among other functions, these proteins are separately involved in the regulation of amyloid beta production, oxidative stress, neuroinflammation, regulation of tau phosphorylation, and regulation of neuronal apoptosis. Our results revealed that Yizhijiannao granule can regulate the expression of various proteins in the temporal lobe of senescence-accelerated mouse prone 8 mice, and may be therapeutically beneficial for the treatment of Alzheimer's disease.
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Affiliation(s)
- Hong Zhu
- Department of Traditional Chinese Medicine, Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Liuyang Luo
- Department of Emergency, Bao-an District Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong Province, China
| | - Sihang Hu
- Department of Traditional Chinese Medicine, Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Keli Dong
- Department of Traditional Chinese Medicine, Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Guangcheng Li
- Department of Traditional Chinese Medicine, Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Ting Zhang
- Department of Traditional Chinese Medicine, Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
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15
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Klaus C, Kaemmerer E, Reinartz A, Schneider U, Plum P, Jeon MK, Hose J, Hartmann F, Schnölzer M, Wagner N, Kopitz J, Gassler N. TP53 status regulates ACSL5-induced expression of mitochondrial mortalin in enterocytes and colorectal adenocarcinomas. Cell Tissue Res 2014; 357:267-78. [PMID: 24770931 DOI: 10.1007/s00441-014-1826-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/23/2014] [Indexed: 12/25/2022]
Abstract
Acyl-CoA synthetase 5 (ACSL5), a mitochondrially localized enzyme, catalyzes the synthesis of long-chain fatty acid thioesters and is physiologically involved in pro-apoptotic sensing of enterocytes. The aim of the present study is to identify an ACSL5-dependent regulation of mitochondrially expressed proteins and the characterization of related pathways in normal and diseased human intestinal mucosa. Proteomics of isolated mitochondria from ACSL5 transfectants and CaCo2 controls were performed. ACSL5-dependent protein synthesis was verified with quantitative reverse transcription plus the polymerase chain reaction, Western blotting, short-interfering-RNA-mediated gene silencing and additional cell culture experiments. Lipid changes were analyzed with tandem mass spectrometry. ACSL5-related pathways were characterized in normal mucosa and sporadic adenocarcinomas of the human intestine. In CaCo2 cells transfected with ACSL5, mortalin (HSPA9) was about two-fold increased in mitochondria, whereas cytoplasmic mortalin levels were unchanged. Disturbance of acyl-CoA/sphingolipid metabolism, induced by ACSL5 over-expression, was characterized as crucial. ACSL5-related over-expression of mitochondrial mortalin was found in HEK293 and Lovo (wild-type TP53 [tumor protein p53]) and CaCo2 (p53-negative; TP53 mutated) cells but not in Colo320DM cells (mutated TP53). In normal human intestinal mucosa, an increasing gradient of both ACSL5 and mortalin from bottom to top was observed, whereas p53 (wild-type TP53) decreased. In sporadic intestinal adenocarcinomas with strong p53 immunostaining (mutated TP53), ACSL5-related mortalin expression was heterogeneous. ACSL5-induced mitochondrial mortalin expression is assumed to be a stress response to ACSL5-related changes in lipid metabolism and is regulated by the TP53 status. Uncoupling of ACSL5 and mitochondrial mortalin by mutated TP53 could be important in colorectal carcinogenesis.
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Affiliation(s)
- Christina Klaus
- Institute of Pathology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
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Boquete MT, Bermúdez-Crespo J, Aboal JR, Carballeira A, Fernández JÁ. Assessing the effects of heavy metal contamination on the proteome of the moss Pseudoscleropodium purum cross-transplanted between different areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:2191-2200. [PMID: 24043506 DOI: 10.1007/s11356-013-2141-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/06/2013] [Indexed: 06/02/2023]
Abstract
Protein expression was assessed in samples of Pseudoscleropodium purum cross-transplanted between one unpolluted (UNP) and two polluted (POLL) sites. Firstly, the level of expression (LE) of 17 proteins differed between native mosses from both types of sites, but differences were only maintained throughout the experiment for 5 of them. The LE of these five proteins changed over time in mosses transplanted from UNP to POLL and vice versa, becoming similar to that in autotransplants. However, these changes occurred slower than changes in the heavy metal concentrations measured in the same samples, and therefore they were not related to atmospheric pollution. Although the proteins identified were associated with moss metabolism, the expected growth reduction in samples autotransplanted within POLL (as a result of the down-regulation of photosynthesis-related proteins), did not occur. This supports the hypothesis that mosses growing in polluted areas adapt to heavy metal pollution and are able to reduce/overcome their toxic effects (i.e., reduced growth). Nevertheless, further specific research must be carried out to identify the proteins involved in this type of response, as lack of information on the bryophyte genome precludes us from reaching further conclusions.
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Affiliation(s)
- M Teresa Boquete
- Ecología, Facultad de Biología, Universidad de Santiago de Compostela, Avda Lope Gómez de Marzoa s/n, Santiago de Compostela, 15782, Spain.
| | - José Bermúdez-Crespo
- Genética, Facultad de Biología, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Jesús R Aboal
- Ecología, Facultad de Biología, Universidad de Santiago de Compostela, Avda Lope Gómez de Marzoa s/n, Santiago de Compostela, 15782, Spain
| | - Alejo Carballeira
- Ecología, Facultad de Biología, Universidad de Santiago de Compostela, Avda Lope Gómez de Marzoa s/n, Santiago de Compostela, 15782, Spain
| | - J Ángel Fernández
- Ecología, Facultad de Biología, Universidad de Santiago de Compostela, Avda Lope Gómez de Marzoa s/n, Santiago de Compostela, 15782, Spain
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17
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Hanneken M, König S. Horizontal comparative fluorescence two-dimensional gel electrophoresis for improved spot coordinate detection. Electrophoresis 2014; 35:1118-21. [DOI: 10.1002/elps.201300507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Marina Hanneken
- Integrated Functional Genomics; Interdisciplinary Center for Clinical Research; University of Münster; Germany
| | - Simone König
- Integrated Functional Genomics; Interdisciplinary Center for Clinical Research; University of Münster; Germany
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18
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Marzban G, Herndl A, Maghuly F, Katinger H, Laimer M. Mapping of fruit allergens by 2D electrophoresis and immunodetection. Expert Rev Proteomics 2014; 5:61-75. [DOI: 10.1586/14789450.5.1.61] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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20
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LIANG XU, WANG JINGRONG, WONG KAMWAIV, HSIAO WENLUAN, ZHOU HUA, JIANG ZHIHONG, KAM KINTINGR, LIU LIANG. Optimization of 2-dimensional gel electrophoresis for proteomic studies of solid tumor tissue samples. Mol Med Rep 2013; 9:626-32. [DOI: 10.3892/mmr.2013.1815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/16/2013] [Indexed: 11/05/2022] Open
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21
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Wöhlbrand L, Trautwein K, Rabus R. Proteomic tools for environmental microbiology-A roadmap from sample preparation to protein identification and quantification. Proteomics 2013; 13:2700-30. [DOI: 10.1002/pmic.201300175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Kathleen Trautwein
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
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22
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Moche M, Albrecht D, Maaß S, Hecker M, Westermeier R, Büttner K. The new horizon in 2D electrophoresis: New technology to increase resolution and sensitivity. Electrophoresis 2013; 34:1510-8. [DOI: 10.1002/elps.201200618] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/18/2013] [Accepted: 02/14/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Martin Moche
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Sandra Maaß
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | | | - Knut Büttner
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
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23
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Reicheltová Z, Májek P, Riedel T, Suttnar J, Dyr JE. Simplified platelet sample preparation for SDS-PAGE-based proteomic studies. Proteomics Clin Appl 2013; 6:374-81. [PMID: 22641369 DOI: 10.1002/prca.201100101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE The goal of this study was to design an easy and simple protocol for platelet isolation and sample preparation for proteomic studies based on 2DE (IEF-SDS-PAGE) followed by Coomassie blue staining. EXPERIMENTAL DESIGN Blood was collected by venipuncture into tubes coated with EDTA and platelet-rich plasma (PRP) was immediately obtained by centrifugation. PRP was stored refrigerated in closed Falcon tubes for 0, 1, 2, 3, 5, and 7 days and platelets were isolated by centrifugation. 2DE gels were stained with colloidal Coomassie blue stain and evaluated using the Progenesis SameSpots software. Spots that differed significantly in the gels of fresh and stored platelet samples were excised, digested with trypsin, and further analyzed using nanoLC-MS/MS. RESULTS During the 7-day follow-up period, we found 20 spots that differed significantly (ANOVA p <0.05). During the first 2 days of PRP storage in test tubes, however, only nine spots significantly differed in all donors. In these spots, we identified 14 different proteins. CONCLUSIONS AND CLINICAL RELEVANCE In conclusion, for proteome investigations, whenever it is not feasible to prepare washed platelets immediately after blood collection, the EDTA-anticoagulated PRP can be stored in test tubes at 4°C for up to 2 days for the platelet proteome investigation.
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Ortiz A, Richa L, Defer C, Dernis D, Huart JJ, Tokarski C, Rolando C. Proteomics applied to transfusion plasma: the beginning of the story. Vox Sang 2013; 104:275-91. [PMID: 23438183 DOI: 10.1111/j.1423-0410.2012.01663.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
'Safe blood' is and has always been the major concern in transfusion medicine. Plasma can undergo virus inactivation treatments based on physicochemical, photochemical or thermal methodologies for pathogen inactivation. The validation of these treatments is essentially based on clottability assays and clotting factors' titration; however, their impact on plasma proteins at the molecular level has not yet been evaluated. Proteomics appears as particularly adapted to identify, to localize and, consequently, to correlate these modifications to the biological activity change. At the crossroads of biology and analytical sciences, proteomics is the large-scale study of proteins in tissues, physiological fluids or cells at a given moment and in a precise environment. The proteomic strategy is based on a set of methodologies involving separative techniques like mono- and bidimensional gel electrophoresis and chromatography, analytical techniques, especially mass spectrometry, and bioinformatics. Even if plasma has been extensively studied since the very beginning of proteomics, its application to transfusion medicine has just begun. In the first part of this review, we present the principles of proteomics analysis. Then, we propose a state of the art of proteomics applied to plasma analysis. Finally, the use of proteomics for the evaluation of the impact of storage conditions and pathogen inactivation treatments applied to transfusion plasma and for the evaluation of therapeutic protein fractionated is discussed.
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Affiliation(s)
- A Ortiz
- USR CNRS 3290, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique (MSAP), Université de Lille 1, Sciences et Technologie, Villeneuve d'Ascq, France
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25
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Seikrit C, Henkel C, van Roeyen CRC, Bokemeyer D, Eitner F, Martin IV, Boor P, Knuchel R, Meyer HE, Muller-Newen G, Eriksson U, Floege J, Ostendorf T. Biological responses to PDGF-AA versus PDGF-CC in renal fibroblasts. Nephrol Dial Transplant 2012; 28:889-900. [DOI: 10.1093/ndt/gfs509] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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26
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Koutsonas A, Carstesen D, Henkel C, Walter P, Thumann G, Weinberger AWA. Effects of coagulation on the autofluorescence pattern of ARPE-19 cells: an in vitro study. Ophthalmic Res 2012; 49:11-9. [PMID: 22964483 DOI: 10.1159/000341740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 06/13/2012] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Changes in fundus autofluorescence (AF) are observed in various retinal disorders. Lipofuscin accumulation within the retinal pigment epithelium (RPE) is a source of fundus AF (FAF); however, the causes of short-term increases in FAF observed in inflammatory conditions or after laser treatment are unknown. Here, we describe an RPE cell culture model that is useful for investigations of FAF. METHODS ARPE-19 cells were cultured in 2-well chamber slides. Cells were exposed to isolated rabbit photoreceptor outer segments (POS) to mimic in vivo phagocytic activity. The AF of RPE cells exposed to POS was measured before and after focal coagulation of the cultures. AF was measured over a period of 4 weeks. Cell lysates were examined by two-dimensional (2D) gel electrophoresis and mass spectrometry analysis. RESULTS The exposure of ARPE cells to POS did not lead to increased AF; however, after coagulation, cells exposed to POS showed a statistically significant increase in AF (p < 0.05). 2D electrophoresis of the cell lysates revealed changes in 3 proteins. One of these proteins, identified by mass spectrometry as ezrin-radixin-moesin-binding phosphoprotein 50, was reduced in the coagulated cell population. CONCLUSIONS We have established an in vitro model of RPE cells in culture that can be used to evaluate the development of AF and changes in cellular proteins that accompany laser photocoagulation.
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Affiliation(s)
- Antonis Koutsonas
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
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27
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Föcking M, Chen WQ, Dicker P, Dunn MJ, Lubec G, Cotter DR. Proteomic analysis of human hippocampus shows differential protein expression in the different hippocampal subfields. Proteomics 2012; 12:2477-81. [DOI: 10.1002/pmic.201200031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Melanie Föcking
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Wei-Qiang Chen
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Patrick Dicker
- Department of Epidemiology; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Michael J. Dunn
- Proteome Research Centre; UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences; Dublin; Ireland
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - David R. Cotter
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
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28
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Pogorelova TN, Orlov VI, Gunko VO. New approaches to molecular diagnostics of prenatal pathology. Bull Exp Biol Med 2012; 151:567-70. [PMID: 22462047 DOI: 10.1007/s10517-011-1384-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Analysis of the spectrum of amniotic fluid proteins in physiological and abnormal pregnancy using proteomic analysis allowed detection of a number of difference proteins, that are absent or, alternatively, appear in gestosis. Among absent proteins, there were NADPH-dependent carbonyl reductase, epidermal fatty acid-binding protein, haptoglobin, calgranulins A and B. In contrast to proteomic spectrum of amniotic fluid in physiological pregnancy, 7 new proteins appear during gestosis, 3 of them were identified: C area of immunoglobulin K-chain, breast cancer metastasis suppressor-1, and protein-1 containing AIG2-like domain. Possible effects of revealed differences in proteomic spectrum on development of main disturbances during gestosis are discussed. Difference proteins detected in amniotic fluid may serve as gestosis markers.
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Affiliation(s)
- T N Pogorelova
- Rostov Institute of Obstetrics and Pediatrics, Federal Agency for High-Technological Medical Care, Rostov-on-Don, Russia.
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29
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Kim H, Goo E, Kang Y, Kim J, Hwang I. Regulation of universal stress protein genes by quorum sensing and RpoS in Burkholderia glumae. J Bacteriol 2012; 194:982-92. [PMID: 22178971 PMCID: PMC3294795 DOI: 10.1128/jb.06396-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 12/08/2011] [Indexed: 11/20/2022] Open
Abstract
Burkholderia glumae possesses a quorum-sensing (QS) system mediated by N-octanoyl-homoserine lactone (C(8)-HSL) and its cognate receptor TofR. TofR/C(8)-HSL regulates the expression of a transcriptional regulator, qsmR. We identified one of the universal stress proteins (Usps), Usp2, from a genome-wide analysis of QS-dependent proteomes of B. glumae. In the whole genome of B. glumae BGR1, 11 usp genes (usp1 to usp11) were identified. Among the stress conditions tested, usp1 and usp2 mutants died 1 h after heat shock stress, whereas the other usp mutants and the wild-type strain survived for more than 3 h at 45°C. The expressions of all usp genes were positively regulated by QS, directly by QsmR. In addition, the expressions of usp1 and usp2 were dependent on RpoS in the stationary phase, as confirmed by the direct binding of RpoS-RNA holoenzyme to the promoter regions of the usp1 and usp2 genes. The expression of usp1 was upregulated upon a temperature shift from 37°C to either 28°C or 45°C, whereas the expression of usp2 was independent of temperature stress. This indicates that the regulation of usp1 and usp2 expression is different from what is known about Escherichia coli. Compared to the diverse roles of Usps in E. coli, Usps in B. glumae are dedicated to heat shock stress.
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Affiliation(s)
- Hongsup Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yongsung Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jinwoo Kim
- Department of Applied Biology, Gyeongsang National University, Jinju, Republic of Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J Bacteriol 2012; 194:1552-61. [PMID: 22228732 DOI: 10.1128/jb.06429-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This dynamic proteome study describes the physiology of growth and survival of Deinococcus geothermalis, in conditions simulating paper machine waters being aerobic, warm, and low in carbon and manganese. The industrial environment of this species differs from its natural habitats, geothermal springs and deep ocean subsurfaces, by being highly exposed to oxygen. Quantitative proteome analysis using two-dimensional gel electrophoresis and bioinformatic tools showed expression change for 165 proteins, from which 47 were assigned to a function. We propose that D. geothermalis grew and survived in aerobic conditions by channeling central carbon metabolism to pathways where mainly NADPH rather than NADH was retrieved from the carbon source. A major part of the carbon substrate was converted into succinate, which was not a fermentation product but likely served combating reactive oxygen species (ROS). Transition from growth to nongrowth resulted in downregulation of the oxidative phosphorylation observed as reduced expression of V-type ATPase responsible for ATP synthesis in D. geothermalis. The battle against oxidative stress was seen as upregulation of superoxide dismutase (Mn dependent) and catalase, as well as several protein repair enzymes, including FeS cluster assembly proteins of the iron-sulfur cluster assembly protein system, peptidylprolyl isomerase, and chaperones. Addition of soluble Mn reinitiated respiration and proliferation with concomitant acidification, indicating that aerobic metabolism was restricted by access to manganese. We conclude that D. geothermalis prefers to combat ROS using manganese-dependent enzymes, but when manganese is not available central carbon metabolism is used to produce ROS neutralizing metabolites at the expense of high utilization of carbon substrate.
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Abstract
2D DIGE, two-dimensional difference gel electrophoresis, is a technology used to study the protein expression on two-dimensional gels. Protein samples are labeled with different color fluorescent dyes designed not to affect the relative migration of proteins during electrophoresis. Here, we describe the practical procedures necessary to perform a 2D DIGE experiment for a muscle tissue protein extract followed by CyDye DIGE fluors minimal labeling and the analysis of 2D DIGE gels for the assessment of quantitative differences.
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Affiliation(s)
- Cecilia Gelfi
- Dipartimento di Scienze e Tecnologie Biomediche, Università degli Studi di Milano, Segrate, Italy.
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32
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Vlad C, Lindner K, Karreman C, Schildknecht S, Leist M, Tomczyk N, Rontree J, Langridge J, Danzer K, Ciossek T, Petre A, Gross ML, Hengerer B, Przybylski M. Autoproteolytic fragments are intermediates in the oligomerization/aggregation of the Parkinson's disease protein alpha-synuclein as revealed by ion mobility mass spectrometry. Chembiochem 2011; 12:2740-4. [PMID: 22162214 DOI: 10.1002/cbic.201100569] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Indexed: 12/29/2022]
Abstract
Gas-phase protein separation by ion mobility: With its ability to separate the Parkinson's disease protein α-synuclein and its autoproteolytic products-despite the small concentrations of the latter-ion-mobility MS has enabled the characterization of intermediate fragments in in vitro oligomerization-aggregation. In particular, a possible key fragment, the highly aggregating C-terminal fragment, αSyn(72-140), has been revealed.
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Affiliation(s)
- Camelia Vlad
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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Gangadharan B, Antrobus R, Chittenden D, Rossa J, Bapat M, Klenerman P, Barnes E, Dwek RA, Zitzmann N. New approaches for biomarker discovery: the search for liver fibrosis markers in hepatitis C patients. J Proteome Res 2011; 10:2643-50. [PMID: 21410221 PMCID: PMC3089987 DOI: 10.1021/pr101077c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Indexed: 12/12/2022]
Abstract
Despite many shortcomings, liver biopsy is regarded as the gold standard for assessing liver fibrosis. A less invasive and equally or more reliable approach would constitute a major advancement in the field. Proteomics can aid discovery of novel serological markers and these proteins can be measured in patient blood. A major challenge of discovering biomarkers in serum is the presence of highly abundant serum proteins, which restricts the levels of total protein loaded onto gels and limits the detection of low abundance features. To overcome this problem, we used two-dimensional gel electrophoresis (2-DE) over a narrow pH 3-5.6 range since this lies outside the range of highly abundant albumin, transferrin and immunoglobulins. In addition, we used in-solution isoelectric focusing followed by SDS-PAGE to find biomarkers in hepatitis C induced liver cirrhosis. Using the pH 3-5.6 range for 2-DE, we achieved improved representation of low abundance features and enhanced separation. We found in-solution isoelectric focusing to be beneficial for analyzing basic, high molecular weight proteins. Using this method, the beta chains of both complement C3 and C4 were found to decrease in serum from hepatitis C patients with cirrhosis, a change not observed previously by 2-DE. We present two proteomics approaches that can aid in the discovery of clinical biomarkers in various diseases and discuss how these approaches have helped to identify 23 novel biomarkers for hepatic fibrosis.
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Affiliation(s)
- Bevin Gangadharan
- Oxford Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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35
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Wölfler MM, Meinhold-Heerlein IM, Söhngen L, Rath W, Knüchel R, Neulen J, Maass N, Henkel C. Two-dimensional gel electrophoresis in peritoneal fluid samples identifies differential protein regulation in patients suffering from peritoneal or ovarian endometriosis. Fertil Steril 2011; 95:2764-8. [PMID: 21497343 DOI: 10.1016/j.fertnstert.2011.03.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/06/2011] [Accepted: 03/21/2011] [Indexed: 11/27/2022]
Abstract
Endometriosis is determined by local and systemic proinflammatory dysregulation and therefore differential protein expression in peritoneal fluid (PF). Of highest interest is lesion formation and the establishment and persistence of endometriosis. In this study we analyzed well-characterized PF samples of patients with ovarian or peritoneal endometriosis and compared them to control samples. We found 11 proteins differentially regulated, of which some might play a key role in the pathogenesis of endometriosis.
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Affiliation(s)
- Monika M Wölfler
- Department of Obstetrics and Gynecology, Medical Faculty of RWTH Aachen University, Aachen, Germany.
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Osiri JK, Shadpour H, Witek MA, Soper SA. Integrated multifunctional microfluidics for automated proteome analyses. Top Curr Chem (Cham) 2011; 304:261-94. [PMID: 21678138 DOI: 10.1007/128_2011_152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device integration. In this chapter, we will focus exclusively on the front-end processing microfluidic devices and systems for proteome processing, and not on the interface technology of these platforms to mass spectrometry due to the extensive reviews that already exist on these types of interfaces.
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Affiliation(s)
- John K Osiri
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70817, USA
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Goo E, Kang Y, Kim H, Hwang I. Proteomic analysis of quorum sensing-dependent proteins in Burkholderia glumae. J Proteome Res 2010; 9:3184-99. [PMID: 20408571 DOI: 10.1021/pr100045n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Burkholderia glumae, the causal agent of bacterial rice grain rot, utilizes quorum sensing (QS) systems that rely on N-octanoyl homoserine lactone (synthesized by TofI) and its cognate receptor TofR to activate toxoflavin biosynthesis genes and an IclR-type transcriptional regulator gene, qsmR. Since QS is essential for B. glumae pathogenicity, we analyzed the QS-dependent proteome by 2-dimensional gel electrophoresis. A total of 79 proteins, including previously known QS-dependent proteins, were differentially expressed between the wild-type BGR1 and the tofI mutant BGS2 strains. Among this set, 59 proteins were found in the extracellular fraction, and 20 were cytoplasmic. Thirty-four proteins, including lipase and proteases, were secreted through the type II secretion system (T2SS). Real-time RT-PCR analysis showed that the corresponding genes of the 49 extracellular and 13 intracellular proteins are regulated by QS at the transcriptional level. The T2SS, encoded by 12 general secretion pathway (gsp) genes with 3 independent transcriptional units, was controlled by QS. beta-Glucuronidase activity analysis of gsp::Tn3-gusA gene fusions and electrophoretic mobility shift assays revealed that the expression of gsp genes is directly regulated by QsmR. T2SS-defective mutants exhibited reduced virulence, indicating that the T2SS-dependent extracellular proteins play important roles in B. glumae virulence.
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Affiliation(s)
- Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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Kim HR, Han RX, Wakayama T, Park CS, Jin DI. Aberrant protein expression in the placenta of cloned mouse derived from embryonic stem cell. Placenta 2010; 31:853-9. [DOI: 10.1016/j.placenta.2010.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/13/2010] [Accepted: 07/13/2010] [Indexed: 12/23/2022]
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Chevalier F. Highlights on the capacities of "Gel-based" proteomics. Proteome Sci 2010; 8:23. [PMID: 20426826 PMCID: PMC2873371 DOI: 10.1186/1477-5956-8-23] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 04/28/2010] [Indexed: 11/18/2022] Open
Abstract
Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.
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Piette F, D'Amico S, Struvay C, Mazzucchelli G, Renaut J, Tutino ML, Danchin A, Leprince P, Feller G. Proteomics of life at low temperatures: trigger factor is the primary chaperone in the Antarctic bacteriumPseudoalteromonas haloplanktisTAC125. Mol Microbiol 2010; 76:120-32. [DOI: 10.1111/j.1365-2958.2010.07084.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rénert AF, Leprince P, Dieu M, Renaut J, Raes M, Bours V, Chapelle JP, Piette J, Merville MP, Fillet M. The proapoptotic C16-ceramide-dependent pathway requires the death-promoting factor Btf in colon adenocarcinoma cells. J Proteome Res 2010; 8:4810-22. [PMID: 19705920 DOI: 10.1021/pr9005316] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ceramides are central molecules in sphingolipid metabolism. They are involved in the regulation of cancer-cell growth, differentiation, senescence and apoptosis. To better understand how these secondary messengers induce their biological effects, adenocarcinoma cells (HCT116) were treated with exogenous long-chain ceramides (C16-ceramide) in order to mimic endogenous sphingolipids. This treatment induced a decrease of cell viability partly due to apoptosis as shown by PARP cleavage and a decrease of pro-caspase 3. Two-dimensional differential in-gel electrophoresis (2D-DIGE) revealed the differential expression of 51 proteins in response to C16-ceramide. These proteins are notably involved in cell proliferation, apoptosis, protein transport and transcriptional regulation. Among them, the cell death-promoting factor Btf was found to be implicated in the apoptotic signal triggered by ceramide. In adenocarcinoma cells, Btf regulates apoptosis related proteins such as Mdm2, p53, BAX and pBcl-2 and thus plays an important role in the ceramide mediated cell death. These findings bring new insight into the proapoptotic ceramide-dependent signaling pathway.
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Affiliation(s)
- Anne-Françoise Rénert
- GIGA Signal Transduction, Unit of Medical Chemistry, University of Liège, Sart-Tilman, Belgium
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Segovia-Gamboa NC, Chávez-Munguía B, Medina-Flores Y, Cázares-Raga FE, Hernández-Ramírez VI, Martínez-Palomo A, Talamás-Rohana P. Entamoeba invadens, encystation process and enolase. Exp Parasitol 2010; 125:63-9. [PMID: 20045689 DOI: 10.1016/j.exppara.2009.12.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 11/25/2022]
Abstract
The reptilian parasite Entamoeba invadens is accepted as a model for the study of the Entamoeba encystation process. Here we describe the production and characterization of a mAb (B4F2), generated against a component of the E. invadens cyst wall. This mAb specifically recognizes a 48-kDa protein present in cytoplasmic vesicles of cells encysting for 24 h. In mature cysts (96 h), the antigen was detected on the cyst surface. By two-dimensional electrophoresis and mass spectrometry analysis, the B4F2 specific antigen was identified as enolase. Levels of enolase mRNA were increased in encysting cells and the B4F2 mAb was found to inhibit cyst formation. Therefore, these results strongly suggest a new role for enolase in E. invadens encystation, and the B4F2 mAb will be useful tool to study its role in the differentiation process.
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Affiliation(s)
- Norma Cristina Segovia-Gamboa
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Zacatenco, 07360 Mexico City, Mexico
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Westermeier R, Schickle H. The current state of the art in high-resolution two-dimensional electrophoresis. Arch Physiol Biochem 2009; 115:279-85. [PMID: 19874117 DOI: 10.3109/13813450903338090] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of the "proteomes" of human cells, tissues, and body fluids is a big challenge, and several highly sophisticated workflow approaches are pursued to achieve as comprehensive information as possible. Initially proteome analysis was exclusively based on the gel-based workflow, employing two-dimensional electrophoresis of protein extracts followed by mass spectrometry of the tryptic peptide digests of protein spots. Meanwhile several additional proteomics workflows are applied, which are mostly based on separation and analysis of tryptic peptides without separating the protein mixture. However, direct information on quantitative and qualitative changes of protein expressions can only be obtained by methods operating on the protein level, no other method can replace two-dimensional electrophoresis. In this review we compile the different techniques of high-resolution two-dimensional electrophoresis and their further developments to increase the degree of reliance of the method.
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Comparative proteomic analysis on Salmonella Gallinarum and Salmonella Enteritidis exploring proteins that may incorporate host adaptation in poultry. J Proteomics 2009; 72:815-21. [DOI: 10.1016/j.jprot.2009.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 04/22/2009] [Accepted: 05/18/2009] [Indexed: 11/18/2022]
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Marcellin E, Gruber CW, Archer C, Craik DJ, Nielsen LK. Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicus. Proteome Sci 2009; 7:13. [PMID: 19327162 PMCID: PMC2670282 DOI: 10.1186/1477-5956-7-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 03/28/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is a commensal of horses and an opportunistic pathogen in many animals and humans. Some strains produce copious amounts of hyaluronic acid, making S. zooepidemicus an important industrial microorganism for the production of this valuable biopolymer used in the pharmaceutical and cosmetic industry. Encapsulation by hyaluronic acid is considered an important virulence factor in other streptococci, though the importance in S. zooepidemicus remains poorly understood. Proteomics may provide a better understanding of virulence factors in S. zooepidemicus, facilitate the design of better diagnostics and treatments, and guide engineering of superior production strains. RESULTS Using hyaluronidase to remove the capsule and by optimising cellular lysis, a reference map for S. zooepidemicus was completed. This protocol significantly increased protein recovery, allowing for visualisation of 682 spots and the identification of 86 proteins using mass spectrometry (LC-ESI-MS/MS and MALDI-TOF/TOF); of which 16 were membrane proteins. CONCLUSION The data presented constitute the first reference map for S. zooepidemicus and provide new information on the identity and characteristics of the more abundantly expressed proteins.
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Affiliation(s)
- Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Australia.
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Starita-Geribaldi M. Selection of pH ranges in 2DE. Methods Mol Biol 2009; 519:31-45. [PMID: 19381575 DOI: 10.1007/978-1-59745-281-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This chapter describes the technical improvements of the two-dimensional electrophoresis pattern resulting of an optimized pH range in the first dimension. Various types of pH gradients are available. Different strategies can be applied in order to select the pH ranges for the exploration of a proteome. The resulting gels are analysed for their background, resolution, sensitivity in relation with the sample complexity. As the complete dynamic range of protein expression cannot be visualized, the high loading capacity of immobilized narrow pH gradients can be used. The limitations and possible enhancements are discussed.
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Affiliation(s)
- Mireille Starita-Geribaldi
- Departement des Sciences Biologiques, UFR d'Odontologie, Pôle Universitaire Saint-Jean d'Angely, 24 avenue des Diables Bleus, 06357, Nice cedex, 4, France
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Abstract
Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry is currently the workhorse for the majority of ongoing proteome projects. Although alternative/complementary technologies, such as MudPIT, ICAT, or protein arrays, have emerged recently, there is up to now no technology that matches 2-DE in its ability for routine parallel expression profiling of large sets of complex protein mixtures. 2-DE delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or post-translational modifications. High-resolution 2-DE can resolve up to 5,000 proteins simultaneously ( approximately 2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Today's 2-DE technology with IPGs has largely overcome the former limitations of carrier ampholyte-based 2-DE with respect to reproducibility, handling, resolution, and separation of very acidic or basic proteins. Current research to further advance 2-DE technology has focused on improved solubilization/separation of hydrophobic proteins, display of low abundance proteins, and reliable protein quantitation by fluorescent dye technologies. Here, we provide a comprehensive protocol of the current high-resolution 2-DE technology with IPGs for proteome analysis and describe in detail the individual steps of this technique, i.e., sample preparation and protein solubilization, isoelectric focusing in IPG strips, IPG strip equilibration, and casting and running of multiple SDS gels. Last but not the least, a section on how to circumvent the major pitfalls is included.
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Abstract
About 30 years ago two-dimensional gel electrophoresis (2DE) was developed independently by Klose and O'Farrell representing the combination of two orthogonal separation techniques. In the first dimension the proteins are separated by isoelectric focusing (IEF) according to their isoelectric point. In the second dimension proteins are separated according to their electrophoretic mobility by conventional SDS-PAGE. For IEF two different techniques, immobilized pH gradient (IPG) and carrier-ampholyte-based IEF (CA-based IEF), respectively, are currently applied. With a resolution of up to 10,000 protein spots in one gel, 2DE offers a huge potential to give a comprehensive overview of the proteins present in the examined system. In combination with image analysis and mass spectrometry 2DE is still the method of choice to analyse complex protein samples.In this chapter we provide detailed protocols for both 2DE systems and give an overview about the latest developments including the two-dimensional difference gel electrophoresis (DIGE) system.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstr. 150, D-44780, Bochum, Germany
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