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Swain IX, Kresak AM. Proteins Involved in Focal Cell Adhesion and Podosome Formation Are Differentially Expressed during Colorectal Tumorigenesis in AOM-Treated Rats. Cancers (Basel) 2024; 16:1678. [PMID: 38730628 PMCID: PMC11083089 DOI: 10.3390/cancers16091678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Colorectal tumorigenesis involves the development of aberrant crypt foci (ACF) or preneoplastic lesions, representing the earliest morphological lesion visible in colon cancer. The purpose of this study was to determine changes in protein expression in carcinogen-induced ACF as they mature and transform into adenomas. Protein expression profiles of azoxymethane (AOM)-induced F344 rat colon ACF and adenomas were compared at four time points, 4 (control), 8, 16, and 24 weeks post AOM administration (n = 9/group), with time points correlating with induction and transformation events. At each time point, micro-dissected ACF and/or adenoma tissues were analyzed across multiple quantitative two-dimensional (2D-DIGE) gels using a Cy-dye labeling technique and a pooled internal standard to quantify expression changes with statistical confidence. Western blot and subsequent network pathway mapping were used to confirm and elucidate differentially expressed (p ≤ 0.05) proteins, including changes in vinculin (Vcl; p = 0.007), scinderin (Scin; p = 0.02), and profilin (Pfn1; p = 0.01), By determining protein expression changes in ACF as they mature and transform into adenomas, a "baseline" of altered regulatory proteins associated with adenocarcinoma development in this model has been elucidated. These data will enable future studies aimed at biomarker identification and understanding the molecular biology of intestinal tumorigenesis and adenocarcinoma maturation under varying intestinal conditions.
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Affiliation(s)
- Ian X. Swain
- Department of Pathology, School of Medicine, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA;
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2
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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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3
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Chang X, Ma M, Chen L, Song Z, Zhao Z, Shen W, Jiang H, Wu Y, Fan M, Wu H. Identification and Characterization of Elevated Expression of Transferrin and Its Receptor TfR1 in Mouse Models of Depression. Brain Sci 2022; 12:1267. [PMID: 36291201 PMCID: PMC9599150 DOI: 10.3390/brainsci12101267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Depression has become one of the severe mental disorders threatening global human health. In this study, we first used the proteomics approach to obtain the differentially expressed proteins in the liver between naive control and chronic social defeat stress (CSDS) induced depressed mice. We have identified the upregulation of iron binding protein transferrin (TF) in the liver, the peripheral blood, and the brain in CSDS-exposed mice. Furthermore, bioinformatics analysis of the Gene Expression Omnibus (GEO) database from various mouse models of depression revealed the significantly upregulated transcripts of TF and its receptor TfR1 in multiple brain regions in depressed mice. We also used the recombinant TF administration via the tail vein to detect its permeability through the blood-brain barrier (BBB). We demonstrated the permeability of peripheral TF into the brain through the BBB. Together, these results identified the elevated expression of TF and its receptor TfR1 in both peripheral liver and the central brain in CSDS-induced depressed mice, and peripheral administration of TF can be transported into the brain through the BBB. Therefore, our data provide a compelling information for understanding the potential role and mechanisms of the cross-talk between the liver and the brain in stress-induced depression.
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Affiliation(s)
- Xin Chang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Mengxin Ma
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Liping Chen
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Zhihong Song
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Zhe Zhao
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Wei Shen
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Huihui Jiang
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Yan Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Ming Fan
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
- School of Information Science & Engineering, Lanzhou University, Lanzhou 730000, China
| | - Haitao Wu
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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5
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Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
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6
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Development of high-performance two-dimensional gel electrophoresis for human hair shaft proteome. PLoS One 2019; 14:e0213947. [PMID: 30889197 PMCID: PMC6424392 DOI: 10.1371/journal.pone.0213947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/04/2019] [Indexed: 11/19/2022] Open
Abstract
The primary components of human hair shaft—keratin and keratin-associated proteins (KAPs), together with their cross-linked networks—are the underlying reason for its rigid structure. It is therefore requisite to overcome the obstacle of hair insolubility and establish a reliable protocol for the proteome analysis of this accessible specimen. The present study employed an alkaline-based method for the efficient isolation of hair proteins and subsequently examined them using gel-based proteomics. The introduction of two proteomic protocols, namely the conventional and modified protocol, have resulted in the detection of more than 400 protein spots on the two-dimensional gel electrophoresis (2DE). When compared, the modified protocol is deemed to improve overall reproducibility, whilst offering a quick overview of the total protein distribution of hair. The development of this high-performance protocol is hoped to provide a new approach for hair analysis, which could possibly lead to the discovery of biomarkers for hair in health and diseases in the future.
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7
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Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations. Methods Mol Biol 2019; 1977:83-97. [PMID: 30980324 DOI: 10.1007/978-1-4939-9232-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.
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Wu X, Xu C, Wang W. Reduction and Alkylation of Proteins in 2D Gel Electrophoresis: Before or after Isoelectric Focusing? Front Chem 2017; 5:59. [PMID: 28861411 PMCID: PMC5559430 DOI: 10.3389/fchem.2017.00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/02/2017] [Indexed: 01/11/2023] Open
Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Chenhui Xu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
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Chemonges S, Gupta R, Mills PC, Kopp SR, Sadowski P. Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum. Proteome Sci 2017; 15:11. [PMID: 28615994 PMCID: PMC5466729 DOI: 10.1186/s12953-017-0119-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 06/02/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological changes and disease states. The objective of this study was to develop a robust and comprehensive method to characterise the circulating acellular proteome in ovine serum. METHODS Serum samples from healthy sheep were subjected to shotgun proteomic analysis using nano liquid chromatography nano electrospray ionisation tandem mass spectrometry (nanoLC-nanoESI-MS/MS) on a quadrupole time-of-flight instrument (TripleTOF® 5600+, SCIEX). Proteins were identified using ProteinPilot™ (SCIEX) and Mascot (Matrix Science) software based on a minimum of two unmodified highly scoring unique peptides per protein at a false discovery rate (FDR) of 1% software by searching a subset of the Universal Protein Resource Knowledgebase (UniProtKB) database (http://www.uniprot.org). PeptideShaker (CompOmics, VIB-UGent) searches were used to validate protein identifications from ProteinPilot™ and Mascot. RESULTS ProteinPilot™ and Mascot identified 245 and 379 protein groups (IDs), respectively, and PeptideShaker validated 133 protein IDs from the entire dataset. Since Mascot software is considered the industry standard and identified the most proteins, these were analysed using the Protein ANalysis THrough Evolutionary Relationships (PANTHER) classification tool revealing the association of 349 genes with 127 protein pathway hits. These data are available via ProteomeXchange with identifier PXD004989. CONCLUSIONS These results demonstrated for the first time the feasibility of characterising the ovine circulating acellular proteome using nanoLC-nanoESI-MS/MS. This peptide spectral data contributes to a protein library that can be used to identify a wide range of proteins in ovine serum.
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Affiliation(s)
- Saul Chemonges
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Rajesh Gupta
- Proteomics and Small Molecule Mass Spectrometry, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Paul C. Mills
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Steven R. Kopp
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Pawel Sadowski
- Proteomics and Small Molecule Mass Spectrometry, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
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10
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O'Doherty PJ, Khan A, Johnson AJ, Rogers PJ, Bailey TD, Wu MJ. Proteomic response to linoleic acid hydroperoxide in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:3752509. [PMID: 28449083 DOI: 10.1093/femsyr/fox022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
Yeast AP-1 transcription factor (Yap1p) and the enigmatic oxidoreductases Oye2p and Oye3p are involved in counteracting lipid oxidants and their unsaturated breakdown products. In order to uncover the response to linoleic acid hydroperoxide (LoaOOH) and the roles of Oye2p, Oye3p and Yap1p, we carried out proteomic analysis of the homozygous deletion mutants oye3Δ, oye2Δ and yap1Δ alongside the diploid parent strain BY4743. The findings demonstrate that deletion of YAP1 narrowed the response to LoaOOH, as the number of proteins differentially expressed in yap1Δ was 70% of that observed in BY4743. The role of Yap1p in regulating the major yeast peroxiredoxin Tsa1p was demonstrated by the decreased expression of Tsa1p in yap1Δ. The levels of Ahp1p and Hsp31p, previously shown to be regulated by Yap1p, were increased in LoaOOH-treated yap1Δ, indicating their expression is also regulated by another transcription factor(s). Relative to BY4743, protein expression differed in oye3Δ and oye2Δ under LoaOOH, underscored by superoxide dismutase (Sod1p), multiple heat shock proteins (Hsp60p, Ssa1p, and Sse1p), the flavodoxin-like protein Pst2p and the actin stabiliser tropomyosin (Tpm1p). Proteins associated with glycolysis were increased in all strains following treatment with LoaOOH. Together, the dataset reveals, for the first time, the yeast proteomic response to LoaOOH, highlighting the significance of carbohydrate metabolism, as well as distinction between the roles of Oye3p, Oye2p and Yap1p.
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Affiliation(s)
- Patrick J O'Doherty
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Alamgir Khan
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney NSW 2109 Australia
| | - Adam J Johnson
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Peter J Rogers
- School of Biomolecular and Physical Sciences, Griffith University, Nathan QLD 4111, Australia
| | - Trevor D Bailey
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Ming J Wu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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11
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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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12
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Satoh R, Teshima R, Kitta K, Lang GH, Schegg K, Blumenthal K, Hicks L, Labory-Carcenac B, Rouquié D, Herman RA, Herouet-Guicheney C, Ladics GS, McClain S, Poulsen LK, Privalle L, Ward JM, Doerrer N, Rascle JB. Inter-laboratory optimization of protein extraction, separation, and fluorescent detection of endogenous rice allergens. Biosci Biotechnol Biochem 2016; 80:2198-2207. [PMID: 27399872 PMCID: PMC5062055 DOI: 10.1080/09168451.2016.1206810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In rice, several allergens have been identified such as the non-specific lipid transfer protein-1, the α-amylase/trypsin-inhibitors, the α-globulin, the 33 kDa glyoxalase I (Gly I), the 52-63 kDa globulin, and the granule-bound starch synthetase. The goal of the present study was to define optimal rice extraction and detection methods that would allow a sensitive and reproducible measure of several classes of known rice allergens. In a three-laboratory ring-trial experiment, several protein extraction methods were first compared and analyzed by 1D multiplexed SDS-PAGE. In a second phase, an inter-laboratory validation of 2D-DIGE analysis was conducted in five independent laboratories, focusing on three rice allergens (52 kDa globulin, 33 kDa glyoxalase I, and 14-16 kDa α-amylase/trypsin inhibitor family members). The results of the present study indicate that a combination of 1D multiplexed SDS-PAGE and 2D-DIGE methods would be recommended to quantify the various rice allergens.
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Affiliation(s)
- Rie Satoh
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Reiko Teshima
- b Division of Novel Foods and Immunochemistry , National Institute of Health Sciences , Tokyo , Japan
| | - Kazumi Kitta
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Gang-Hua Lang
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Kathleen Schegg
- c Nevada Proteomics Center , University of Nevada Reno , Reno , NV , USA
| | - Kenneth Blumenthal
- d Formerly at Department of Biochemistry , State University of New York at Buffalo , Buffalo , NY , USA
| | - Leslie Hicks
- e Formerly at Proteomics & Mass Spectrometry Facility , Donald Danforth Plant Science Center , St. Louis , MI , USA
| | | | - David Rouquié
- f Bayer S.A.S., Bayer CropScience , Sophia Antipolis , France
| | - Rod A Herman
- g Dow AgroSciences LLC , Indianapolis , IN , USA
| | | | - Gregory S Ladics
- i DuPont Haskell Global Centers for Health and Environmental Sciences , Newark , DE , USA
| | - Scott McClain
- j Syngenta Crop Protection, LLC , Research Triangle Park , NC , USA
| | - Lars K Poulsen
- k Allergy Clinic , Copenhagen University Hospital at Gentofte , Copenhagen , Denmark
| | - Laura Privalle
- l Regulatory Science , Formerly at BASF Plant Science , Research Triangle Park , NC , USA
| | - Jason M Ward
- m Regulatory Division, Product Characterization Center , Formerly at Monsanto Co. , St. Louis , MO , USA
| | - Nancy Doerrer
- n Protein Allergenicity Technical Committee , ILSI Health and Environmental Sciences Institute (HESI) , Washington , DC , USA
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Makert GR, Vorbrüggen S, Krautwald-Junghanns ME, Voss M, Sohn K, Buschmann T, Ulbert S. A method to identify protein antigens of Dermanyssus gallinae for the protection of birds from poultry mites. Parasitol Res 2016; 115:2705-13. [PMID: 27026505 DOI: 10.1007/s00436-016-5017-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
Abstract
The poultry red mite (PRM) Dermanyssus gallinae causes high economic losses and is among the most important parasites in poultry farming worldwide. Different chemical, physical, and biological strategies try to control the expansion of PRM. However, effective solutions to this problem still have to be found. Here, we present a method for the development of an immunological control strategy, based on the identification of mite protein antigens which elicit antibodies with anti-mite activity in the immunized chicken. Hens were immunized with different PRM protein extracts formulated with two different adjuvants, and IgY-antibodies were isolated from the eggs. A PRM in vitro feeding assay which used chicken blood spiked with these IgY-preparations was used to detect antibodies which caused PRM mortality. In vitro feeding of mites with IgY isolated from hens immunized with PRM extract formulated with one of the adjuvants showed a statistically significant increase in the mortality as compared to control mites. After the separation of total PRM extracts in two-dimensional gels, several protein spots were recognized by such IgY preparations. Ten protein spots were subjected to mass spectrometry (MS/MS) for the identification of the corresponding proteins. Complete protein sequences were deduced from genomic and transcriptomic assemblies derived from high throughput sequencing of total PRM DNA and RNA. The results may contribute to the development of an immunological control strategy of D. gallinae.
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Affiliation(s)
- Gustavo R Makert
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103, Leipzig, Germany.,Clinic for Birds and Reptiles, Leipzig University, An den Tierkliniken 17, 04103, Leipzig, Germany
| | - Susanne Vorbrüggen
- Clinic for Birds and Reptiles, Leipzig University, An den Tierkliniken 17, 04103, Leipzig, Germany
| | | | - Matthias Voss
- Lohmann Tierzucht GmbH, Am Seedeich 9-11, 27454, Cuxhaven, Germany
| | - Kai Sohn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Tilo Buschmann
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103, Leipzig, Germany
| | - Sebastian Ulbert
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103, Leipzig, Germany.
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Luna C, Alique M, Navalmoral E, Noci MV, Bohorquez-Magro L, Carracedo J, Ramírez R. Aging-associated oxidized albumin promotes cellular senescence and endothelial damage. Clin Interv Aging 2016; 11:225-36. [PMID: 27042026 PMCID: PMC4780186 DOI: 10.2147/cia.s91453] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Increased levels of oxidized proteins with aging have been considered a cardiovascular risk factor. However, it is unclear whether oxidized albumin, which is the most abundant serum protein, induces endothelial damage. The results of this study indicated that with aging processes, the levels of oxidized proteins as well as endothelial microparticles release increased, a novel marker of endothelial damage. Among these, oxidized albumin seems to play a principal role. Through in vitro studies, endothelial cells cultured with oxidized albumin exhibited an increment of endothelial damage markers such as adhesion molecules and apoptosis levels. In addition, albumin oxidation increased the amount of endothelial microparticles that were released. Moreover, endothelial cells with increased oxidative stress undergo senescence. In addition, endothelial cells cultured with oxidized albumin shown a reduction in endothelial cell migration measured by wound healing. As a result, we provide the first evidence that oxidized albumin induces endothelial injury which then contributes to the increase of cardiovascular disease in the elderly subjects.
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Affiliation(s)
- Carlos Luna
- Nephrology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofía University Hospital, Córdoba, Spain
| | - Matilde Alique
- Department of Systems Biology, Physiology Unit, Universidad de Alcalá, Madrid, Spain
| | - Estefanía Navalmoral
- Department of Systems Biology, Physiology Unit, Universidad de Alcalá, Madrid, Spain
| | | | | | - Julia Carracedo
- Nephrology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofía University Hospital, Córdoba, Spain
| | - Rafael Ramírez
- Department of Systems Biology, Physiology Unit, Universidad de Alcalá, Madrid, Spain
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Switzar L, Nicolardi S, Rutten JW, Oberstein SAJL, Aartsma-Rus A, van der Burgt YEM. In-Depth Characterization of Protein Disulfide Bonds by Online Liquid Chromatography-Electrochemistry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:50-8. [PMID: 26369777 PMCID: PMC4686567 DOI: 10.1007/s13361-015-1258-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 05/04/2023]
Abstract
Disulfide bonds are an important class of protein post-translational modifications, yet this structurally crucial modification type is commonly overlooked in mass spectrometry (MS)-based proteomics approaches. Recently, the benefits of online electrochemistry-assisted reduction of protein S-S bonds prior to MS analysis were exemplified by successful characterization of disulfide bonds in peptides and small proteins. In the current study, we have combined liquid chromatography (LC) with electrochemistry (EC) and mass analysis by Fourier transform ion cyclotron resonance (FTICR) MS in an online LC-EC-MS platform to characterize protein disulfide bonds in a bottom-up proteomics workflow. A key advantage of a LC-based strategy is the use of the retention time in identifying both intra- and interpeptide disulfide bonds. This is demonstrated by performing two sequential analyses of a certain protein digest, once without and once with electrochemical reduction. In this way, the "parent" disulfide-linked peptide detected in the first run has a retention time-based correlation with the EC-reduced peptides detected in the second run, thus simplifying disulfide bond mapping. Using this platform, both inter- and intra-disulfide-linked peptides were characterized in two different proteins, ß-lactoglobulin and ribonuclease B. In order to prevent disulfide reshuffling during the digestion process, proteins were digested at a relatively low pH, using (a combination of) the high specificity proteases trypsin and Glu-C. With this approach, disulfide bonds in ß-lactoglobulin and ribonuclease B were comprehensively identified and localized, showing that online LC-EC-MS is a useful tool for the characterization of protein disulfide bonds.
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Affiliation(s)
- Linda Switzar
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
- , Albinusdreef 2, Postzone S3, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Julie W Rutten
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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Hromadkova L, Kupcik R, Jankovicova B, Rousar T, Ripova D, Bilkova Z. Difficulties associated with the structural analysis of proteins susceptible to form aggregates: The case of Tau protein as a biomarker of Alzheimer's disease. J Sep Sci 2015; 39:799-807. [PMID: 26644024 DOI: 10.1002/jssc.201501045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/05/2022]
Abstract
Mass spectrometry coupled with bioaffinity separation techniques is considered a powerful tool for studying protein interactions. This work is focused on epitope analysis of tau protein, which contains two VQIXXK aggregation motifs regarded as crucial elements in the formation of paired helical filaments, the main pathological characteristics of Alzheimer's disease. To identify major immunogenic structures, the epitope extraction technique utilizing protein fragmentation and magnetic microparticles functionalized with specific antibodies was applied. However, the natural adhesiveness of some newly generated peptide fragments devalued the experimental results. Beside presumed peptide fragment specific to applied monoclonal anti-tau antibodies, the epitope extraction repeatedly revealed inter alia tryptic fragment 299-HVPGGGSVQIVYKPVDLSK-317 containing the fibril-forming motif 306-VQIVYK-311. The tryptic fragment pro-aggregation and hydrophobic properties that might contribute to adsorption phenomenon were examined by Thioflavin S and reversed-phase chromatography. Several conventional approaches to reduce the non-specific fragment sorption onto the magnetic particle surface were performed, however with no effect. To avoid methodological complications, we introduced an innovative approach based on altered proteolytic digestion. Simultaneous fragmentation of tau protein by two immobilized proteases differing in the cleavage specificity (TPCK-trypsin and α-chymotrypsin) led to the disruption of motif responsible for undesirable adhesiveness and enabled us to obtain undistorted structural data.
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Affiliation(s)
- Lenka Hromadkova
- Department of Neurobiology and AD Center, National Institute of Mental Health, Klecany, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Rudolf Kupcik
- Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Barbora Jankovicova
- Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Tomas Rousar
- Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Daniela Ripova
- Department of Neurobiology and AD Center, National Institute of Mental Health, Klecany, Czech Republic
| | - Zuzana Bilkova
- Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
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17
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Berthold T, Schubert N, Muschter S, Rohr M, Wesche J, Reil A, Bux J, Bakchoul T, Greinacher A. HNA antibody-mediated neutrophil aggregation is dependent on serine protease activity. Vox Sang 2015; 109:366-74. [PMID: 26084778 DOI: 10.1111/vox.12292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVES Transfusion-related acute lung injury (TRALI) is often caused by antibodies against human neutrophil alloantigen-2 (HNA-2) and HNA-3a. Neutrophil aggregation is considered as a major cause of TRALI, but little is known about how HNA antibodies initiate this process. We explored mechanisms involved in neutrophil aggregation induced by HNA-2 and HNA-3a antibodies. MATERIALS AND METHODS Isolated neutrophils were pretreated with broad-spectrum or specific inhibitors against different cell functions or proteases. Granulocyte agglutination test (GAT) was performed with serially diluted anti-HNA-2 and anti-HNA-3a plasmas or control plasma, and reactivity was evaluated microscopically. Reactive oxygen species (ROS) production in neutrophils was investigated using a lucigenin-based chemiluminescence assay. RESULTS HNA-2 and HNA-3a antibody-mediated neutrophil aggregation was inhibited by pretreatment with formaldehyde, iodoacetamide and the serine protease inhibitors Pefabloc-SC, N-p-tosyl-L-phenylalanine chloromethyl ketone (TPCK) and Nα-tosyl-L-lysine chloromethyl ketone hydrochloride (TLCK). In contrast, inhibition of actin polymerization, respiratory burst, cysteine proteases, metalloproteases or aspartic proteases did not affect neutrophil aggregation. Furthermore, HNA-3a antibodies did not directly cause ROS production in neutrophils. CONCLUSION Aggregation of neutrophils induced by HNA-2 and HNA-3a antibodies is an active process and depends on trypsin- or chymotrypsin-like serine proteases but is not dependent on the production of ROS. These findings may open new prospects for the pharmacologic prevention of neutrophil-associated acute lung injury.
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Affiliation(s)
- T Berthold
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - N Schubert
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - S Muschter
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - M Rohr
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - J Wesche
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - A Reil
- Deutsches Rotes Kreuz - Blutspendedienst West, Hagen, Germany
| | - J Bux
- Ruhr Universität Bochum, Bochum, Germany
| | - T Bakchoul
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - A Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
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Maserti B, Podda A, Giorgetti L, Del Carratore R, Chevret D, Migheli Q. Proteome changes during yeast-like and pseudohyphal growth in the biofilm-forming yeast Pichia fermentans. Amino Acids 2015; 47:1091-106. [PMID: 25743163 DOI: 10.1007/s00726-015-1933-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 02/03/2015] [Indexed: 12/25/2022]
Abstract
The Pichia fermentans strain DISAABA 726 is a biofilm-forming yeast that has been proposed as biocontrol agent to control brown rot on apple. How ever, when inoculated on peach, strain 726 shows yeast-like to pseudohyphal transition coupled to a pathogenic behaviour. To identify the proteins potentially involved in such transition process, a comparative proteome analysis of P. fermentans 726 developed on peach (filamentous growth) vs apple (yeast-like growth) was carried out using two-dimensional gel electrophoresis coupled with mass spectrometry analysis. The proteome comparison was also performed between the two different cell morphologies induced in a liquid medium amended with urea (yeast-like cells) or methionine (filamentous cells) to exclude fruit tissue impact on the transition. Seventy-three protein spots showed significant variations in abundance (±twofold, p < 0.01, confidence intervals 99 %) between pseudohyphal vs yeast-like morphology produced on fruits. Among them, 30 proteins changed their levels when the two morphologies were developed in liquid medium. The identified proteins belong to several pathways and functions, such as glycolysis, amino acid synthesis, chaperones, and signalling transduction. The possible role of a group of proteins belonging to the carbohydrate pathway in the metabolic re-organisation during P. fermentans dimorphic transition is discussed.
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Affiliation(s)
- Biancaelena Maserti
- CNR-IPSP, Consiglio Nazionale delle Ricerche-Dipartimento di Scienze Bio-Agroalimentari, Istituto per la Protezione Sostenibile delle Piante, Area della Ricerca CNR, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Florence, Italy,
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Fasoli E, Righetti PG, Moltrasio D, D'Amato A. Extensive heterogeneity of human urokinase, as detected by two-dimensional mapping. Anal Chem 2015; 87:1509-13. [PMID: 25525926 DOI: 10.1021/ac5037796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urokinase (uPA, urinary plasminogen activator) is a serine protease belonging to the peptidase S1 family. Specifically, uPA cleaves the zymogen plasminogen into the active form (plasmin), which then degrades the fibrin clots. It is widely used as a fibrinolytic agent in thrombolytic therapy and it is also used clinically as a thrombolytic agent. It can be administered to improve the drainage of complicated pleural effusions and empyemas and it is the most effective drug in myocardial infarction. The enzyme was originally identified in human urine for its ability to catalyze the transformation of plasminogen into its active form (plasmin), which degrades fibrin and extracellular matrix components. The present report deals with the analysis and characterization of this preparation.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano , Via Mancinelli 7, Milano 20131, Italy
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20
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Separation of basic proteins from Leishmania using a combination of Free flow electrophoresis (FFE) and 2D electrophoresis (2-DE) under basic conditions. Methods Mol Biol 2015; 1201:247-59. [PMID: 25388119 DOI: 10.1007/978-1-4939-1438-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Basic proteins, an important class of proteins in intracellular organisms such as Leishmania, are usually underrepresented on 2D gels. This chapter describes a method combining basic proteins fractionation using Free flow electrophoresis in isoelectric focusing mode (IEF-FFE) followed by protein separation using two-dimensional gel electrophoresis (2-DE) in basic conditions. The combination of these two techniques represents a great improvement for the visualization of Leishmania proteins with basic pI using 2D gels.
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21
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Abstract
Sample preparation is one of the key technologies for successful two-dimensional electrophoresis (2DE). Due to the great diversity of protein sample types and sources, no single sample preparation method works with all proteins; for any sample the optimum procedure must be determined empirically. This review is meant to provide a broad overview of the most important principles in sample preparation in order to avoid a multitude of possible pitfalls. Sample preparation protocols from the expert in the field were screened and evaluated. On the basis of these protocols and my own comprehensive practical experience important guidelines are given in this review. The presented guidelines will facilitate straightforward protocol development for researchers new to gel-based proteomics. In addition the available choices are rationalized in order to successfully prepare a protein sample for 2DE separations. The strategies described here are not limited to 2DE and can also be applied to other protein separation techniques.
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Affiliation(s)
- Anton Posch
- Bio-Rad Laboratories GmbH , Heidemannstrasse Munich , Germany
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22
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Paggi RA, Giménez MI, De Castro RE, Cesari A. A simple technique to improve the resolution of membrane acidic proteins of the haloarchaeon Haloferax volcanii by 2D electrophoresis. Electrophoresis 2014; 35:3518-22. [PMID: 25224925 DOI: 10.1002/elps.201400407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/06/2022]
Abstract
Proteins present in the archaeal cell envelope play key roles in a variety of processes necessary for survival in extreme environments. The haloarchaeon Haloferax volcanii is a good model for membrane proteomic studies because its genome sequence is known, it can be genetically manipulated, and a number of studies at the "omics" level have been performed in this organism. This work reports an easy strategy to improve the resolution of acidic membrane proteins from H. volcanii by 2DE. The method is based on the solubilization, delipidation, and salt removal from membrane proteins. Due to the abundance of the S-layer glycoprotein (SLG) in membrane protein extracts, other proteins from the envelope are consequently underrepresented. Thus, a protocol to reduce the amount of the SLG by EDTA treatment was applied and 11 cm narrow range pH (3.9-5.1) IPG strips were used to fractionate the remaining proteins. Using this method, horizontal streaking was substantially decreased and at least 75 defined spots (20% of the predicted membrane proteome within this pI/Mw range) were reproducibly detected. Two of these spots were identified as thermosome subunit 1 and NADH dehydrogenase from H. volcanii, confirming that proteins from the membrane fraction were enriched. Removal of the SLG from membrane protein extracts can be applied to increase protein load for 2DE as well as for other proteomic methods.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, UNMdP-CONICET, Mar del Plata, Argentina
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23
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Saraygord-Afshari N, Naderi-Manesh H, Naderi M. Enhanced reproducibility of the human gel-based tear proteome maps in the presence of di-(2-hydroxyethyl) disulfide. Biotechnol Appl Biochem 2014; 61:660-7. [PMID: 24575874 DOI: 10.1002/bab.1221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/21/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Neda Saraygord-Afshari
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Mostafa Naderi
- Bina Eye Hospital; Tehran Iran
- Department of Ophthalmology; Baqiyatallah University of Medical Sciences; Tehran Iran
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24
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Oliveira BM, Coorssen JR, Martins-de-Souza D. 2DE: the phoenix of proteomics. J Proteomics 2014; 104:140-50. [PMID: 24704856 DOI: 10.1016/j.jprot.2014.03.035] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022]
Abstract
UNLABELLED Given the rapid developments in mass spectrometry (MS) in terms of sensitivity, mass accuracy, and throughput, some have suggested that two-dimensional gel electrophoresis (2DE) may no longer be a method of choice for proteomic analyses. However, as recognition of issues with these newer shotgun-MS approaches grows, there is a fresh and growing regard for the maturity of 2DE-MS as a genuine top-down analytical approach, particularly as it resolves thousands of intact protein species in a single run, enabling the simultaneous analysis of total protein complement, including isoforms and post-translational modifications. Given the strengths of both, it is most appropriate to view these as complementary or at least parallel approaches: as proteins encompass a myriad of physico-chemical properties, and the real aim is to explore proteomes as deeply as possible, all available resolving strategies must be considered in terms of the complexity encountered. It is time to critically and constructively focus on the optimization and integration of existing techniques rather than simplistically suggesting that one should replace the other. Our intention here is thus to present an overview of protein resolving techniques, focusing on milestones associated with 2DE, including pros, cons, advances and variations, in particular relative to shotgun proteomic approaches. BIOLOGICAL SIGNIFICANCE Proteomic researchers recognize the importance of 2DE in the history of proteomics. But the latest developments in mass spectrometry-based techniques have led some researchers to retire 2DE in their labs. However, we argue here that 2DE-MS is a genuine top-down analytical approach. The significance of this discussion is to make proteomic researchers aware of the importance of this technique in a proteomic pipeline. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Bruno M Oliveira
- Catarinense Federal Institute, Videira Campus, Videira, SC, Brazil
| | - Jens R Coorssen
- Dept. of Molecular Physiology, School of Medicine, University of Western Sydney, Australia; UWS Molecular Medicine Research Group, University of Western Sydney, Australia.
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil; Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, Brazil; Dept. of Psychiatry and Psychotherapy, Ludwig Maximilians University (LMU), Munich, Germany.
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25
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Wright EP, Partridge MA, Padula MP, Gauci VJ, Malladi CS, Coorssen JR. Top-down proteomics: enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection. Proteomics 2014; 14:872-89. [PMID: 24452924 DOI: 10.1002/pmic.201300424] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/01/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023]
Abstract
The large-scale resolution and detection of proteins from complex native mixtures is fundamental to quantitative proteomic analyses. Comprehensive analyses depend on careful tissue handling and quantitative protein extraction and assessment. To most effectively link these analyses with an understanding of underlying molecular mechanisms, it is critical that all protein types - isoforms, splice variants and those with functionally important PTMs - are quantitatively extracted with high reproducibility. Methodological details concerning protein extraction and resolution using 2DE are discussed with reference to current in-gel protein detection limits. We confirm a significant increase in total protein, and establish that extraction, resolution and detection of phospho- and glycoproteins are improved following automated frozen disruption relative to manual homogenisation. The quality of 2DE protein resolution is established using third-dimension separations and 'deep imaging'; substantially more proteins/protein species than previously realised are actually resolved by 2DE. Thus, the key issue for effective proteome analyses is most likely to be detection, not resolution. Thus, these systematic methodological and technical advances further solidify the role of 2DE in top-down proteomics. By routinely assessing as much proteomic data from a sample as possible, 2DE enables more detailed and critical insights into molecular mechanisms underlying different physiological states.
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Affiliation(s)
- Elise P Wright
- Department of Molecular Physiology, Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW, Australia
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26
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Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2014; 3:129-42. [PMID: 16445357 DOI: 10.1586/14789450.3.1.129] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D electrophoresis (2DE) is a prominent separation method for complex proteomes. Although recent advances have increased the utility of this method in quantitative proteomics studies, many sources of variance still exist. This review discusses the post-electrophoretic sources of variance in current 2DE analysis. The essential improvements in protein visualization and software algorithms that have made 2DE a leading quantitative proteomics method are briefly reviewed. A number of shortcomings in the post-electrophoretic analysis of 2DE data that require further attention are highlighted. Topics discussed include protein visualization and image acquisition, internal standards and normalization methods, background subtraction algorithms, normality of distribution, and the need for standardized tests for the evaluation of 2DE analysis software packages.
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Affiliation(s)
- Asa M Wheelock
- Kyoto University, Bioinformatics Center, Institute for Chemical Research, Uji, Kyoto, 611-0011, Japan.
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27
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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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28
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Pigosso LL, Parente AFA, Coelho ASG, Silva LP, Borges CL, Bailão AM, Soares CMDA. Comparative proteomics in the genus Paracoccidioides. Fungal Genet Biol 2013; 60:87-100. [PMID: 23911955 DOI: 10.1016/j.fgb.2013.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The genus Paracoccidioides comprises a complex of phylogenetic species of dimorphic pathogenic fungi, the etiologic agents of paracoccidioidomycosis (PCM), a disease confined to Latin America and of marked relevance in its endemic areas due to its high frequency and severity. The members of the Paracoccidioides genus are distributed in distinct phylogenetic species (S1, PS2, PS3 and 01-like) that potentially differ in their biochemical and molecular characteristics. In this work, we performed the proteomic characterization of different members of the genus Paracoccidioides. We compared the proteomic profiles of Pb01 (01-like), Pb2 (PS2), Pb339 (S1) and PbEPM83 (PS3) using 2D electrophoresis and mass spectrometry. The proteins/isoforms were selected based on the staining intensity of the spots as determined by image analysis. The proteins/isoforms were in-gel digested and identified by peptide mass fingerprinting and ion fragmentation. A total of 714 spots were detected, of which 343 were analyzed. From these spots, 301 represented differentially expressed proteins/isoforms among the four analyzed isolates, as determined by ANOVA. After applying the FDR correction, a total of 267 spots were determined to be differentially expressed. From the total, 193 proteins/isoforms were identified by PMF and confirmed by ion fragmentation. Comparing the expression profiles of the isolates, the proteins/isoforms that were related to glycolysis/gluconeogenesis and to alcohol fermentation were more abundant in Pb01 than in other representatives of the genus Paracoccidioides, indicating ahigher use of anaerobic pathways for energy production. Those enzymes related to the oxidative stress response were more abundant in Pb01, Pb2 and Pb339, indicating a better response to ROS in these members of the Paracoccidioides complex. The enzymes of the pentose phosphate pathway were abundant in Pb2. Antigenic proteins, such as GP43 and a 27-kDa antigenic protein, were less abundant in Pb01 and Pb2. The proteomic profile indicates metabolic differences among the analyzed members of the Paracoccidioides genus.
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Affiliation(s)
- Laurine Lacerda Pigosso
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
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29
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Abstract
First described nearly 20 years before Marc Wilkins coined the term 'proteomics', two-dimensional electrophoresis (2DGE) is still in adolescence (as is the field of proteomics). It is well recognised that two dimensions are insufficient for deconvoluting the complexity of even the simplest of proteomes, and that 2DGE can only be part of more elaborate 'multidimensional' schemes. As upstream dimensions continue to be developed, the potential of 2DGE may be further realised. Although orthogonal electrophoresis is unrivalled in its ability to resolve the total protein constituency of cells, arraying the 1500 or so most abundant proteins becomes of diminishing importance. Similar to looking into the sun in an effort to see sunspots, candidate biomarkers of extremely low abundance are concealed amid the myriad of proteins of higher abundance. The procedural complexity and inability to automate 2DGE seems to be prohibitive to its use in the clinical laboratory, which is an unfortunate consequence as this is where the promise of proteomics must ultimately be fulfilled.
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30
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Islam A, Labbate M, Djordjevic SP, Alam M, Darling A, Melvold J, Holmes AJ, Johura FT, Cravioto A, Charles IG, Stokes HW. Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic. Open Biol 2013; 3:120181. [PMID: 23407641 PMCID: PMC3603452 DOI: 10.1098/rsob.120181] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Of the 200+ serogroups of Vibrio cholerae, only O1 or O139 strains are reported to cause cholera, and mostly in endemic regions. Cholera outbreaks elsewhere are considered to be via importation of pathogenic strains. Using established animal models, we show that diverse V. cholerae strains indigenous to a non-endemic environment (Sydney, Australia), including non-O1/O139 serogroup strains, are able to both colonize the intestine and result in fluid accumulation despite lacking virulence factors believed to be important. Most strains lacked the type three secretion system considered a mediator of diarrhoea in non-O1/O13 V. cholerae. Multi-locus sequence typing (MLST) showed that the Sydney isolates did not form a single clade and were distinct from O1/O139 toxigenic strains. There was no correlation between genetic relatedness and the profile of virulence-associated factors. Current analyses of diseases mediated by V. cholerae focus on endemic regions, with only those strains that possess particular virulence factors considered pathogenic. Our data suggest that factors other than those previously well described are of potential importance in influencing disease outbreaks.
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Affiliation(s)
- Atiqul Islam
- The Ithree Institute, University of Technology, Broadway, Sydney, New South Wales 2007, Australia
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Weber SS, Parente AFA, Borges CL, Parente JA, Bailão AM, de Almeida Soares CM. Analysis of the secretomes of Paracoccidioides mycelia and yeast cells. PLoS One 2012; 7:e52470. [PMID: 23272246 PMCID: PMC3525554 DOI: 10.1371/journal.pone.0052470] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/13/2012] [Indexed: 11/19/2022] Open
Abstract
Paracoccidioides, a complex of several phylogenetic species, is the causative agent of paracoccidioidomycosis. The ability of pathogenic fungi to develop a multifaceted response to the wide variety of stressors found in the host environment is important for virulence and pathogenesis. Extracellular proteins represent key mediators of the host-parasite interaction. To analyze the expression profile of the proteins secreted by Paracoccidioides, Pb01 mycelia and yeast cells, we used a proteomics approach combining two-dimensional electrophoresis with matrix-assisted laser desorption ionization quadrupole time-of-flight mass spectrometry (MALDI-Q-TOF MS/MS). From three biological replicates, 356 and 388 spots were detected, in mycelium and yeast cell secretomes, respectively. In this study, 160 non-redundant proteins/isoforms were indentified, including 30 and 24 proteins preferentially secreted in mycelia and yeast cells, respectively. In silico analyses revealed that 65% of the identified proteins/isoforms were secreted primarily via non-conventional pathways. We also investigated the influence of protein export inhibition in the phagocytosis of Paracoccidioides by macrophages. The addition of Brefeldin A to the culture medium significantly decreased the production of secreted proteins by both Paracoccidioides and internalized yeast cells by macrophages. In contrast, the addition of concentrated culture supernatant to the co-cultivation significantly increased the number of internalized yeast cells by macrophages. Importantly, the proteins detected in the fungal secretome were also identified within macrophages. These results indicate that Paracoccidioides extracellular proteins are important for the fungal interaction with the host.
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Affiliation(s)
- Simone Schneider Weber
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Ana Flávia Alves Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Juliana Alves Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Alexandre Melo Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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Inhibitor of apoptosis protein-like protein-2 as a novel serological biomarker for breast cancer. Int J Mol Sci 2012; 13:16737-50. [PMID: 23222679 PMCID: PMC3546717 DOI: 10.3390/ijms131216737] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/22/2012] [Accepted: 11/30/2012] [Indexed: 11/16/2022] Open
Abstract
Inhibitor of apoptosis protein-like protein-2 (ILP-2) has only been detected in the testis and in lymphoblastoid cells. Although previous studies have not reported the presence of ILP-2 in breast cancer tissues, this study indicates the presence of ILP-2 in breast cancer serum samples. To validate whether ILP-2 is a novel serological biomarker for breast cancer, we conducted two-dimensional gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis on 400 breast cancer serum samples and 40 non-cancer serum samples (i.e., healthy controls). We then performed a Western blot analysis of 10 breast cancer serum samples and 10 non-cancer serum samples. Finally, we analyzed 35 serum samples from healthy controls or subjects with breast cancer, other types of cancer, galactophore hyperplasia or breast cancer post-surgery by using 2DE and enzyme-linked immunosorbent assay. Our results indicate that ILP-2 is a novel breast cancer biomarker in the peripheral blood.
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Reed PW, Densmore A, Bloch RJ. Optimization of large gel 2D electrophoresis for proteomic studies of skeletal muscle. Electrophoresis 2012; 33:1263-70. [PMID: 22589104 DOI: 10.1002/elps.201100642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We describe improved methods for large format, two-dimensional gel electrophoresis (2DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7 M urea and 2 M thiourea, instead of 9 M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2DE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes.
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Affiliation(s)
- Patrick W Reed
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, Department of Physiology, University of Maryland School of Medicine University of Maryland, Baltimore, MD 21201, USA.
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Martínez JL, Luna C, Ramos J. Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS Yeast Res 2012; 12:651-61. [DOI: 10.1111/j.1567-1364.2012.00815.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- José L. Martínez
- Departamento de Microbiología; Universidad de Córdoba; Córdoba; Spain
| | - Carlos Luna
- Departamento de Microbiología; Universidad de Córdoba; Córdoba; Spain
| | - José Ramos
- Departamento de Microbiología; Universidad de Córdoba; Córdoba; Spain
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Millioni R, Polati R, Menini M, Puricelli L, Miuzzo M, Tessari P, Novelli E, Righetti PG, Cecconi D. Polar electrophoresis: shape of two-dimensional maps is as important as size. PLoS One 2012; 7:e30911. [PMID: 22292075 PMCID: PMC3264644 DOI: 10.1371/journal.pone.0030911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/24/2011] [Indexed: 11/19/2022] Open
Abstract
The performance of two-dimensional electrophoresis in conventional gels in Cartesian coordinates (2-DE) vs. polar coordinates (2-PE) is here evaluated. Although 2-DE is performed in much longer Immobiline gels in the first dimension (17 cm) vs. barely 7-cm in 2-PE, an equivalent resolving power is found. Moreover, due to the possibility of running up to seven Immobiline strips in the radial gel format, the reproducibility of spot position is seen to be higher, this resulting in a 20% higher matching efficiency. As an extra bonus, strings of “isobaric” spots (i.e. polypeptides of identical mass with different pI values) are more resolved in the radial gel format, especially in the 10 to 30 kDa region, where the gel area fans out leaving extra space for spot resolution. In conclusion, this novel gel format in the second dimension of 2D gels is seen as an important improvement of this technique, still one of the most popular in proteome analysis.
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Affiliation(s)
| | - Rita Polati
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Michele Menini
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Manuela Miuzzo
- Institute of Neuroscience, National Research Council, Padova, Italy
| | - Paolo Tessari
- Department of Medicine, University of Padova, Padova, Italy
| | - Enrico Novelli
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Legnaro, Italy
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Milano, Italy
| | - Daniela Cecconi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
- * E-mail:
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Giuliano S, Iadarola P, Leva V, Montecucco A, Camerini S, Crescenzi M, Salvini R, Bardoni A. An insight into the abundant proteome of 46BR.1G1 fibroblasts deficient of DNA ligase I. Electrophoresis 2012; 33:307-15. [DOI: 10.1002/elps.201100332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Serena Giuliano
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Paolo Iadarola
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Valentina Leva
- Institute of Molecular Genetics, National Council of Research, Pavia, Italy
| | | | - Serena Camerini
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Marco Crescenzi
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Roberta Salvini
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Anna Bardoni
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
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Kaschani F, Gu C, van der Hoorn RAL. Activity-based protein profiling of infected plants. Methods Mol Biol 2012; 835:47-59. [PMID: 22183646 DOI: 10.1007/978-1-61779-501-5_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Activity-based protein profiling (ABPP) is a powerful analytical method to detect and compare the activity of proteins in proteomes. This is achieved using specific activity-based probes that are often derived from inhibitors and are linked to reporter groups like rhodamine or biotin for fluorescence detection and/or affinity purification, respectively. The probes react with the active site residue of proteins and become covalently and irreversibly attached, facilitating the separation, detection and identification of the labelled proteins. In this protocol we describe all the steps required for labelling, purification and identification of labelled proteins from gels and show how activities in two proteomes can be compared. The identification of serine hydrolases from Arabidopsis plants infected with Botrytis cinerea using the trifunctional probe TriFP is used as an example.
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Affiliation(s)
- Farnusch Kaschani
- The Plant Chemetics Laboratory, Chemical Genomics Centre, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Abstract
MALDI-TOF mass spectrometers are now commonplace and their relative ease of use means that most non-specialist labs can readily access the technology for the rapid and sensitive analysis of biomolecules. One of the main uses of MALDI-TOF-MS is in the identification of proteins, by peptide mass fingerprinting (PMF). Here we describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by 1D or 2D gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and destaining, reduction and alkylation, in-gel trypsin digestion, MALDI-TOF-MS of the tryptic peptides and database searching of the PMF data. Up to 96 protein samples can easily be manually processed at one time by this method.
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Affiliation(s)
- Judith Webster
- Proteomics Research Group, Babraham Institute, Babraham, UK
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39
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Petriz BA, Gomes CP, Rocha LAO, Rezende TMB, Franco OL. Proteomics applied to exercise physiology: A cutting-edge technology. J Cell Physiol 2011; 227:885-98. [DOI: 10.1002/jcp.22809] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Labbate M, Boucher Y, Chowdhury PR, Stokes HW. Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus. BMC Microbiol 2011; 11:253. [PMID: 22093957 PMCID: PMC3262767 DOI: 10.1186/1471-2180-11-253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/18/2011] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 25% of a bacterium's genome may have been acquired by this process over evolutionary periods of time. Successful LGT requires both the physical transfer of DNA and its successful incorporation into the host cell. One system that contributes to this latter step by site-specific recombination is the integron. Integrons are found in many diverse bacterial Genera and is a genetic system ubiquitous in vibrios that captures mobile DNA at a dedicated site. The presence of integron-associated genes, contained within units of mobile DNA called gene cassettes makes up a substantial component of the vibrio genome (1-3%). Little is known about the role of this system since the vast majority of genes in vibrio arrays are highly novel and functions cannot be ascribed. It is generally regarded that strain-specific mobile genes cannot be readily integrated into the cellular machinery since any perturbation of core metabolism is likely to result in a loss of fitness. RESULTS In this study, at least one mobile gene contained within the Vibrio rotiferianus strain DAT722, but lacking close relatives elsewhere, is shown to greatly reduce host fitness when deleted and tested in growth assays. The precise role of the mobile gene product is unknown but impacts on the regulation of outermembrane porins. This demonstrates that strain specific laterally acquired mobile DNA can be integrated rapidly into bacterial networks such that it becomes advantageous for survival and adaptation in changing environments. CONCLUSIONS Mobile genes that are highly strain specific are generally believed to act in isolation. This is because perturbation of existing cell machinery by the acquisition of a new gene by LGT is highly likely to lower fitness. In contrast, we show here that at least one mobile gene, apparently unique to a strain, encodes a product that has integrated into central cellular metabolic processes such that it greatly lowers fitness when lost under those conditions likely to be commonly encountered for the free living cell. This has ramifications for our understanding of the role mobile gene encoded products play in the cell from a systems biology perspective.
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Affiliation(s)
- Maurizio Labbate
- The ithree institute, University of Technology, Sydney. Harris Street and Broadway, Sydney, NSW 2007, Australia
| | - Yan Boucher
- Department of Biological Sciences, University of Alberta. 110 St NW Edmonton, Alberta, T6G 2R3, Canada
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology, Sydney. Harris Street and Broadway, Sydney, NSW 2007, Australia
| | - Hatch W Stokes
- The ithree institute, University of Technology, Sydney. Harris Street and Broadway, Sydney, NSW 2007, Australia
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41
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Parente AFA, Bailão AM, Borges CL, Parente JA, Magalhães AD, Ricart CAO, Soares CMA. Proteomic analysis reveals that iron availability alters the metabolic status of the pathogenic fungus Paracoccidioides brasiliensis. PLoS One 2011; 6:e22810. [PMID: 21829521 PMCID: PMC3145762 DOI: 10.1371/journal.pone.0022810] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 07/04/2011] [Indexed: 11/18/2022] Open
Abstract
Paracoccidioides brasiliensis is a thermodimorphic fungus and the causative agent of paracoccidioidomycosis (PCM). The ability of P. brasiliensis to uptake nutrients is fundamental for growth, but a reduction in the availability of iron and other nutrients is a host defense mechanism many pathogenic fungi must overcome. Thus, fungal mechanisms that scavenge iron from host may contribute to P. brasiliensis virulence. In order to better understand how P. brasiliensis adapts to iron starvation in the host we compared the two-dimensional (2D) gel protein profile of yeast cells during iron starvation to that of iron rich condition. Protein spots were selected for comparative analysis based on the protein staining intensity as determined by image analysis. A total of 1752 protein spots were selected for comparison, and a total of 274 out of the 1752 protein spots were determined to have changed significantly in abundance due to iron depletion. Ninety six of the 274 proteins were grouped into the following functional categories; energy, metabolism, cell rescue, virulence, cell cycle, protein synthesis, protein fate, transcription, cellular communication, and cell fate. A correlation between protein and transcript levels was also discovered using quantitative RT-PCR analysis from RNA obtained from P. brasiliensis under iron restricting conditions and from yeast cells isolated from infected mouse spleens. In addition, western blot analysis and enzyme activity assays validated the differential regulation of proteins identified by 2-D gel analysis. We observed an increase in glycolytic pathway protein regulation while tricarboxylic acid cycle, glyoxylate and methylcitrate cycles, and electron transport chain proteins decreased in abundance under iron limiting conditions. These data suggest a remodeling of P. brasiliensis metabolism by prioritizing iron independent pathways.
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Affiliation(s)
- Ana F. A. Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Alexandre M. Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Clayton L. Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Juliana A. Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Adriana D. Magalhães
- Laboratório de Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Carlos A. O. Ricart
- Laboratório de Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Célia M. A. Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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Piubelli C, Gruber S, El Khoury A, Mathé AA, Domenici E, Carboni L. Nortriptyline influences protein pathways involved in carbohydrate metabolism and actin-related processes in a rat gene-environment model of depression. Eur Neuropsychopharmacol 2011; 21:545-62. [PMID: 21168998 DOI: 10.1016/j.euroneuro.2010.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/24/2010] [Accepted: 11/09/2010] [Indexed: 01/21/2023]
Abstract
Although most available antidepressants increase monoaminergic neurotransmission, their therapeutic efficacy is likely mediated by longer-term molecular adaptations. To investigate the molecular changes induced by chronic antidepressant treatment we analysed proteomic changes in rat pre-frontal/frontal cortex and hippocampus after nortriptyline (NT) administration. A wide-scale analysis of protein expression was performed on the Flinders Sensitive Line (FSL), a genetically-selected rat model of depression, and the control Flinders Resistant Line (FRL). The effect of NT treatment was examined in a gene-environment interaction model, applying maternal separation (MS) to both strains. In the forced swim test, FSL rats were significantly more immobile than FRL animals, whereas NT treatment reduced immobility time. MS alone did not modify immobility time, but it impaired the response to NT in the FSL strain. In the proteomic analysis, in FSL rats NT treatment chiefly modulated cytoskeleton proteins and carbohydrate metabolism. In the FRL strain, changes influenced protein polymerization and intracellular transport. After MS, NT treatment mainly affected proteins in nucleotide metabolism in FSL rats and synaptic transmission and neurite morphogenesis pathways in FRL rats. When the effects of NT treatment and MS were compared between strains, carbohydrate metabolic pathways were predominantly modulated.
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Escitalopram modulates neuron-remodelling proteins in a rat gene-environment interaction model of depression as revealed by proteomics. Part I: genetic background. Int J Neuropsychopharmacol 2011; 14:796-833. [PMID: 21054914 DOI: 10.1017/s1461145710001318] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The wide-scale analysis of protein expression provides a powerful strategy for the molecular exploration of complex pathophysiological mechanisms, such as the response to antidepressants. Using a 2D proteomic approach we investigated the Flinders Sensitive Line (FSL), a genetically selected rat model of depression, and the control Flinders Resistant Line (FRL). To evaluate gene-environment interactions, FSL and FRL pups were separated from their mothers for 3 h (maternal separation, MS), as early-life trauma is considered an important antecedent of depression. All groups were treated with either escitalopram (Esc) admixed to food (25 mg/kg.d) or vehicle for 1 month. At the week 3, forced swim tests were performed. Protein extracts from prefrontal/frontal cortex and hippocampus were separated by 2D electrophoresis. Proteins displaying statistically significant differences in expression levels were identified by mass spectrometry. Immobility time values in the forced swim test were higher in FSL rats and reduced by antidepressant treatment. Moreover, the Esc-induced reduction in immobility time was not detected in MS rats. The impact of genetic background in response to Esc was specifically investigated here. Bioinformatics analyses highlighted gene ontology terms showing tighter associations with the modulated proteins. Esc modulated protein belonging to cytoskeleton organization in FSL; carbohydrate metabolism and intracellular transport in FRL. Proteins differently modulated in the two strains after MS and Esc play a role in cytoskeleton organization, vesicle-mediated transport, apoptosis regulation and macromolecule catabolism. These findings suggest pathways involved in neuronal remodelling as molecular correlates of response to antidepressants in a model of vulnerability.
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Gasperini L, Piubelli C, Carboni L. Proteomics of rat hypothalamus, hippocampus and pre-frontal/frontal cortex after central administration of the neuropeptide PACAP. Mol Biol Rep 2011; 39:2921-35. [PMID: 21687973 DOI: 10.1007/s11033-011-1054-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 06/08/2011] [Indexed: 11/25/2022]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide that exerts pleiotropic functions, acting as a hypophysiotropic factor, a neurotrophic and a neuroprotective agent. The molecular pathways activated by PACAP to exert its physiological roles in brain are incompletely understood. In this study, adrenocorticotropic hormone (ACTH), prolactin, luteinising hormone (LH), follicle-stimulating hormone (FSH), thyroid-stimulating hormone (TSH), brain-derived neurotrophic factor and corticosterone blood levels were determined before and 20, 40, 60, and 120 min after PACAP intracerebroventricular administration. PACAP treatment increased ACTH, corticosterone, LH and FSH blood concentrations, while it decreased TSH levels. A proteomics investigation was carried out in hypothalamus, hippocampus and pre-frontal/frontal cortex (P/FC) using 2-dimensional gel electrophoresis at 120 min, the end-point suggested by studies on PACAP hypophysiotropic activities. Spots showing statistically significant alterations after PACAP treatment were identified by Matrix-assisted laser desorption/ionization-Time of flight mass spectrometry. Identified proteins were consistent with PACAP involvement in different molecular processes in brain. Altered expression levels were observed for proteins involved in cytoskeleton modulation and synaptic plasticity: actin in the hypothalamus; stathmin, dynamin, profilin and cofilin in hippocampus; synapsin in P/FC. Proteins involved in cellular differentiation were also modulated: glutathione-S-transferase α and peroxiredoxin in hippocampus; nucleoside diphosphate kinase in P/FC. Alterations were detected in proteins involved in neuroprotection, neurodegeneration and apoptosis: ubiquitin carboxyl-terminal hydrolase isozyme L1 and heat shock protein 90-β in hypothalamus; α-synuclein in hippocampus; glyceraldehyde-3-phosphate dehydrogenase and prohibitin in P/FC. This proteomics study identified new proteins involved in molecular mechanisms mediating PACAP functions in the central nervous system.
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Affiliation(s)
- Lisa Gasperini
- Neurosciences CEDD, GlaxoSmithKline Medicines Research Centre, Via A Fleming 4, 37135 Verona, Italy
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45
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Gel-based mass spectrometric and computational approaches to the mitochondrial proteome of Neurospora. Fungal Genet Biol 2011; 48:526-36. [DOI: 10.1016/j.fgb.2010.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/24/2010] [Accepted: 11/24/2010] [Indexed: 11/18/2022]
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46
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Giron P, Dayon L, Sanchez JC. Cysteine tagging for MS-based proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:366-395. [PMID: 21500242 DOI: 10.1002/mas.20285] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 05/30/2023]
Abstract
Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.
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Affiliation(s)
- Priscille Giron
- Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, University of Geneva, Geneva, Switzerland
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47
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Regulation of cytoskeleton machinery, neurogenesis and energy metabolism pathways in a rat gene-environment model of depression revealed by proteomic analysis. Neuroscience 2011; 176:349-80. [DOI: 10.1016/j.neuroscience.2010.12.043] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/09/2010] [Indexed: 11/15/2022]
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48
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Jobbins SE, Hill CJ, D'Souza-Basseal JM, Padula MP, Herbert BR, Krockenberger MB. Immunoproteomic approach to elucidating the pathogenesis of cryptococcosis caused by Cryptococcus gattii. J Proteome Res 2010; 9:3832-41. [PMID: 20545298 DOI: 10.1021/pr100028t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cryptococcosis caused by Cryptococcus gattii is a devastating disease of immunocompetent hosts with an incompletely understood pathogenesis. Utilizing an immunoproteomic approach in a naturally occurring koala model of disease, a number of key proteins and pathways are identified in the early and late pathogenesis of cryptococcosis for the first time. In particular, the thioredoxin system appears important in the pathogenesis of cryptococcosis caused by C. gattii VGII.
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Affiliation(s)
- Sarah E Jobbins
- The Faculty of Veterinary Science, the University of Sydney, Australia
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Ishikawa N, Ohlmeier S, Salmenkivi K, Myllärniemi M, Rahman I, Mazur W, Kinnula VL. Hemoglobin α and β are ubiquitous in the human lung, decline in idiopathic pulmonary fibrosis but not in COPD. Respir Res 2010; 11:123. [PMID: 20836851 PMCID: PMC2949726 DOI: 10.1186/1465-9921-11-123] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/13/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are disorders of the lung parenchyma. They share the common denominators of a progressive nature and poor prognosis. The goal was to use non-biased proteomics to discover new markers for these diseases. METHODS Proteomics of fibrotic vs. control lung tissue suggested decreased levels of several spots in the lung specimens of IPF patients, which were identified as Hemoglobin (Hb) α and β monomers and Hbα complexes. The Hbα and β monomers and complexes were investigated in more detail in normal lung and lung specimens of patients with IPF and COPD by immunohistochemistry, morphometry and mass spectrometry (MS). RESULTS Both Hb monomers, in normal lung, were expressed especially in the alveolar epithelium. Levels of Hbα and β monomers and complexes were reduced/lost in IPF but not in the COPD lungs when compared to control lung. MS-analyses revealed Hbα modification at cysteine105 (Cysα105), preventing formation of the Hbα complexes in the IPF lungs. Hbα and Hbβ were expressed as complexes and monomers in the lung tissues, but were secreted into the bronchoalveolar lavage fluid and/or induced sputum supernatants as complexes corresponding to the molecular weight of the Hb tetramer. CONCLUSIONS The abundant expression of the oxygen carrier molecule Hb in the normal lung epithelium and its decline in IPF lung are new findings. The loss of Hb complex formation in IPF warrants further studies and may be considered as a disease-specific modification.
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Affiliation(s)
- Nobuhisa Ishikawa
- Department of Medicine, Pulmonary Division, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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López-Pedrera C, Cuadrado MJ, Herández V, Buendïa P, Aguirre MA, Barbarroja N, Torres LA, Villalba JM, Velasco F, Khamashta M. Proteomic analysis in monocytes of antiphospholipid syndrome patients: deregulation of proteins related to the development of thrombosis. ACTA ACUST UNITED AC 2010; 58:2835-44. [PMID: 18759277 DOI: 10.1002/art.23756] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Antiphospholipid antibodies (aPL) are closely related to the development of thrombosis, but the exact mechanism(s) leading to thrombotic events remains unknown. In this study, using proteomic techniques, we evaluated changes in protein expression of monocytes from patients with antiphospholipid syndrome (APS) related to the pathophysiology of the syndrome. METHODS Fifty-one APS patients were included. They were divided into 2 groups: patients with previous thrombosis, and patients with recurrent spontaneous abortion. As controls, we studied patients with thrombosis but without aPL, and age- and sex-matched healthy subjects. RESULTS The proteins that were more significantly altered among monocytes from APS patients with thrombosis (annexin I, annexin II, protein disulfide isomerase, Nedd8, RhoA proteins, and Hsp60) were functionally related to the induction of a procoagulant state as well as to autoimmune-related responses. Proteins reported to be connected to recurrent spontaneous abortion (e.g., fibrinogen and hemoglobin) were also determined to be significantly deregulated in APS patients without thrombosis. In vitro treatment with IgG fractions purified from the plasma of APS patients with thrombosis changed the pattern of protein expression of normal monocytes in the same way that was observed in vivo for monocytes from APS patients with thrombosis. CONCLUSION For the first time, proteomic analysis has identified novel proteins that may be involved in the pathogenic mechanisms of APS, thus providing potential new targets for pathogenesis-based therapies for the disease.
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