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Dihazi H, Müller CA, Mattes H, Müller GA. Proteomic analysis to improve adequacy of hemo- and peritoneal dialysis: Removal of small and high molecular weight proteins with high- and low-flux filters or a peritoneal membrane. Proteomics Clin Appl 2008; 2:1167-82. [DOI: 10.1002/prca.200780143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Indexed: 11/08/2022]
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Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC - tandem mass spectrometry. Proteome Sci 2008; 6:15. [PMID: 18501002 PMCID: PMC2412861 DOI: 10.1186/1477-5956-6-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 05/23/2008] [Indexed: 01/28/2023] Open
Abstract
Background Proteomic methodologies increasingly have been applied to the kidney to map the renal cortical proteome and to identify global changes in renal proteins induced by diseases such as diabetes. While progress has been made in establishing a renal cortical proteome using 1-D or 2-DE and mass spectrometry, the number of proteins definitively identified by mass spectrometry has remained surprisingly small. Low coverage of the renal cortical proteome as well as our interest in diabetes-induced changes in proteins found in the renal cortex prompted us to perform an in-depth proteomic analysis of mouse renal cortical tissue. Results We report a large scale analysis of mouse renal cortical proteome using SCX prefractionation strategy combined with HPLC – tandem mass spectrometry. High-confidence identification of ~2,000 proteins, including cytoplasmic, nuclear, plasma membrane, extracellular and unknown/unclassified proteins, was obtained by separating tryptic peptides of renal cortical proteins into 60 fractions by SCX prior to LC-MS/MS. The identified proteins represented the renal cortical proteome with no discernible bias due to protein physicochemical properties, subcellular distribution, biological processes, or molecular function. The highest ranked molecular functions were characteristic of tubular epithelium, and included binding, catalytic activity, transporter activity, structural molecule activity, and carrier activity. Comparison of this renal cortical proteome with published human urinary proteomes demonstrated enrichment of renal extracellular, plasma membrane, and lysosomal proteins in the urine, with a lack of intracellular proteins. Comparison of the most abundant proteins based on normalized spectral abundance factor (NSAF) in this dataset versus a published glomerular proteome indicated enrichment of mitochondrial proteins in the former and cytoskeletal proteins in the latter. Conclusion A whole tissue extract of the mouse kidney cortex was analyzed by an unbiased proteomic approach, yielding a dataset of ~2,000 unique proteins identified with strict criteria to ensure a high level of confidence in protein identification. As a result of extracting all proteins from the renal cortex, we identified an exceptionally wide range of renal proteins in terms of pI, MW, hydrophobicity, abundance, and subcellular location. Many of these proteins, such as low-abundance proteins, membrane proteins and proteins with extreme values in pI or MW are traditionally under-represented in 2-DE-based proteomic analysis.
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Abstract
Cells in the renal inner medulla are normally exposed to extraordinarily high levels of NaCl and urea. The osmotic stress causes numerous perturbations because of the hypertonic effect of high NaCl and the direct denaturation of cellular macromolecules by high urea. High NaCl and urea elevate reactive oxygen species, cause cytoskeletal rearrangement, inhibit DNA replication and transcription, inhibit translation, depolarize mitochondria, and damage DNA and proteins. Nevertheless, cells can accommodate by changes that include accumulation of organic osmolytes and increased expression of heat shock proteins. Failure to accommodate results in cell death by apoptosis. Although the adapted cells survive and function, many of the original perturbations persist, and even contribute to signaling the adaptive responses. This review addresses both the perturbing effects of high NaCl and urea and the adaptive responses. We speculate on the sensors of osmolality and document the multiple pathways that signal activation of the transcription factor TonEBP/OREBP, which directs many aspects of adaptation. The facts that numerous cellular functions are altered by hyperosmolality and remain so, even after adaptation, indicate that both the effects of hyperosmolality and adaptation to it involve profound alterations of the state of the cells.
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Dihazi H, Müller GA, Lindner S, Meyer M, Asif AR, Oellerich M, Strutz F. Characterization of Diabetic Nephropathy by Urinary Proteomic Analysis: Identification of a Processed Ubiquitin Form as a Differentially Excreted Protein in Diabetic Nephropathy Patients. Clin Chem 2007; 53:1636-45. [PMID: 17634209 DOI: 10.1373/clinchem.2007.088260] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Background: Identification of markers for prediction of the clinical course of diabetic nephropathy remains a major challenge in disease management. We established a proteomics approach for identification of diabetic nephropathy-related biomarkers in urine.
Methods: We used SELDI-TOF mass spectrometry and SAX2 protein arrays to compare protein profiles from urine of 4 defined patient groups. Samples from patients with type 2 diabetes (DM; n = 45) without nephropathy and without microalbuminuria (DM-WNP), patients with DM with macro- or microalbuminuria (DM-NP; n = 38), patients with proteinuria due to nondiabetic renal disease (n = 34), and healthy controls (n = 45) were analyzed. Anionic exchange, reversed-phase fractionation, gel electrophoresis, and mass spectrometry were used to isolate and identify proteins with high discriminatory power.
Results: A protein with m/z 6188 (P <0.0000004) was strongly released in the urine of healthy controls, patients with proteinuria due to nondiabetic disease, and DM-WNP in contrast to DM-NP patients. An m/z 14 766 protein (P <0.00008) was selectively excreted in the urine of DM-NP patients, whereas the protein with m/z 11 774 (P <0.000004) was significantly excreted by patients with proteinuria and DM-NP. The m/z 11 774 and m/z 14 766 mass peaks were identified as β2-microglobulin and UbA52, a ubiquitin ribosomal fusion protein, respectively. The protein with m/z 6188 was identified as a processed form of ubiquitin.
Conclusion: The release of high amounts of UbA52 in urine of DM-NP patients could serve as a diagnostic marker, whereas the lack of the short form of ubiquitin raises interesting questions about the pathophysiology.
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Affiliation(s)
- Hassan Dihazi
- Department of Nephrology and Rheumatology, Georg-August-University Medical Center, Goettingen, Germany.
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55
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Ozcan S, Yildirim V, Kaya L, Albrecht D, Becher D, Hecker M, Ozcengiz G. Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response. Proteomics 2007; 7:1249-60. [PMID: 17366474 DOI: 10.1002/pmic.200600526] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A 2-D reference map in pI range 3-10 was constructed for the soluble protein fraction of Phanerochaete chrysosporium growing vegetatively under standard conditions. Functional annotation could be made for 517 spots out of 720 that were subjected to MALDI-TOF-MS analysis, according to the specific accession numbers from the P. chrysosporium genomic database. Further analysis of the data revealed 314 distinct ORFs, 118 of which yielded multiple spots on the master gel. Functional classification of the proteins was made according to the eukaryote orthologous groups defined in the organism's genome website. The functional class of PTMs, protein turnover and chaperones was represented with the highest number (63) of the identified ORFs. Six proteins were assigned to the hypothetical proteins and 29 were predicted to have a signal peptide sequence. Subcellular localization predictions were also made for the identified proteins. Of the protein spots detected on the master gel, 380 were found to be probably phosphorylated and 96 of these matched to the identified proteins. The reference map was efficiently used in the identification of the proteins differentially expressed under cadmium and copper stress. Three new ribosomal proteins as well as zinc-containing alcohol dehydrogenase, glucose-6-phosphate isomerase, flavonol/cinnamoyl-CoA reductase, H+-transporting two-sector ATPase, ribosomal protein S7, ribosomal protein S21e, elongation factor EF-1 alpha subunit were demonstrated as the most strongly induced.
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Affiliation(s)
- Servet Ozcan
- Department of Biology, Erciyes University, Kayseri, Turkey
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Park JS, Han KY, Song JA, Ahn KY, Seo HS, Lee J. Escherichia coli malate dehydrogenase, a novel solubility enhancer for heterologous proteins synthesized in Escherichia coli. Biotechnol Lett 2007; 29:1513-8. [PMID: 17549433 DOI: 10.1007/s10529-007-9417-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 05/01/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Using 2-dimensional gel electrophoresis, the Escherichia coli proteome response to a heat-shock stress was analyzed and a 1.6-fold increase of malate dehydrogenase was observed even under the heat-shock condition where the total number of soluble proteins decreased by about 5%. We subsequently demonstrated that, as an N-terminus fusion expression partner, malate dehydrogenase facilitated the folding of, and dramatically increased the solubility of, many aggregation-prone heterologous proteins in E. coli cytoplasm. Therefore, malate dehydrogenase is well suited for production of a biologically active fusion mutant of cutinase (Pseudomonas putida origin) that is currently of considerable to biotechnology and commercial industries.
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Affiliation(s)
- Jin-Seung Park
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul, 136-713, South Korea
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Tilton RG, Haidacher SJ, Lejeune WS, Zhang X, Zhao Y, Kurosky A, Brasier AR, Denner L. Diabetes-induced changes in the renal cortical proteome assessed with two-dimensional gel electrophoresis and mass spectrometry. Proteomics 2007; 7:1729-42. [PMID: 17436268 DOI: 10.1002/pmic.200700017] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To understand the spectrum of proteins affected by diabetes and to characterize molecular functions and biological processes they control, we analyzed the renal cortical proteome of db/db mice using 2-DE combined with MALDI-TOF, MALDI-TOF/TOF, and LC-MS/MS. This approach yielded 278 high confidence identifications whose expression levels were significantly increased or decreased >two-fold by diabetes, of which 170 mapped to gene identifiers representing 147 nonredundant proteins. Gene Ontology classification demonstrated that 80% of these proteins modulated physiological functions, 55% involved metabolism, approximately 25% involved carboxylic and organic acid metabolism, 14% involved biosynthesis or catabolism, and 12% involved fatty acid metabolism. Predominant molecular functions were catalytic (61%), oxidoreductase (20%), and transferase (17%) activities, and nucleotide and ATP binding (11-15%). Twenty eight percent of the proteins identified as significantly altered by diabetes were mitochondrial proteins. The top-ranked network described by Ingenuity Pathway Analysis indicated PPARalpha was the most common node of interaction for the numerous enzymes whose expression levels were influenced by diabetes. These differentially regulated proteins create a foundation for a systems biology exploration of molecular mechanisms underlying the pathophysiology of diabetic nephropathy.
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Affiliation(s)
- Ronald G Tilton
- Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX 77555, USA.
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58
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Dihazi H, Müller C, Asif AR, Flad T, Elmaouhoub A, Müller GA. Whole cell profiling and identification of galectin-1 as a potential marker of renal cell carcinoma. Proteomics Clin Appl 2007; 1:200-14. [DOI: 10.1002/prca.200600481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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59
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Kim Y, Nandakumar MP, Marten MR. Proteome map of Aspergillus nidulans during osmoadaptation. Fungal Genet Biol 2007; 44:886-95. [PMID: 17258477 DOI: 10.1016/j.fgb.2006.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 11/29/2006] [Accepted: 12/03/2006] [Indexed: 02/02/2023]
Abstract
The model filamentous fungus Aspergillus nidulans, when grown in a moderate level of osmolyte (+0.6M KCl), was previously found to have a significantly reduced cell wall elasticity (Biotech Prog, 21:292, 2005). In this study, comparative proteomic analysis via two-dimensional gel electrophoresis (2de) and matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry was used to assess molecular level events associated with this phenomenon. Thirty of 90 differentially expressed proteins were identified. Sequence homology and conserved domains were used to assign probable function to twenty-one proteins currently annotated as "hypothetical." In osmoadapted cells, there was an increased expression of glyceraldehyde-3-phosphate dehydrogenase and aldehyde dehydrogenase, as well as a decreased expression of enolase, suggesting an increased glycerol biosynthesis and decreased use of the TCA cycle. There also was an increased expression of heat shock proteins and Shp1-like protein degradation protein, implicating increased protein turnover. Five novel osmoadaptation proteins of unknown functions were also identified.
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Affiliation(s)
- Yonghyun Kim
- Department of Chemical and Biochemical Engineering, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
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60
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Ramachandra Rao SP, Wassell R, Shaw MA, Sharma K. Profiling of human mesangial cell subproteomes reveals a role for calmodulin in glucose uptake. Am J Physiol Renal Physiol 2007; 292:F1182-9. [PMID: 17200159 DOI: 10.1152/ajprenal.00268.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Proteomics combined with cell fractionation was used to identify proteins regulated by high glucose (HG) in human mesangial cells (HMC). Total membrane and cytosolic fraction proteins derived from HMC after 7 days of HG exposure were resolved by a two-dimensional gel electrophoresis approach. DeCyder software was used to analyze the HG-induced protein spot dysregulation. In the membrane subproteome, of the 92 spots that were matched across all gels, HG induced significant downregulation of only 4 protein spots. The dysregulated spots from the membrane subproteome included binding protein (BiP), calreticulin precursor protein, a 63-kDa transmembrane protein from a ER/Golgi intermediate, and beta-subunit of collagen proline 4-hydroxylase. In the cytosolic subproteome, of the 122 spots that were matched across all gels, HG induced downregulation of 3 protein spots and upregulation of 2 protein spots significantly. Enolase 1, annexin VI, and gamma(2)-actin were decreased, whereas heat shock protein-70 kDa and calmodulin (CaM) were increased. Further confocal microscopy and Western immunoblotting of mesangial cells validated the increase in CaM. Immunoblotting of diabetic mouse and rat kidneys exhibited a marked increase in CaM at both early and late stages of diabetes, reflecting the potential physiological relevance of CaM upregulation. CaM-specific inhibitors blocked glucose transport stimulated by transforming growth factor-beta and insulin in mesangial cells. In conclusion, using a combination of cell fractionation and protein expression profiling, we identified a cohort of HG-dysregulated proteins in the HMC and identified a critical and as yet unrecognized role for CaM in glucose transport in mesangial cells.
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Affiliation(s)
- Satish P Ramachandra Rao
- Dept. of Medicine, Center for Novel Therapies for Kidney Disease, Suite 365 Jefferson Alumni Hall, 1020 Locust St., Philadelphia, PA 19107, USA.
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Burkhart BA, Kennett SB, Archer TK. Osmotic stress-dependent repression is mediated by histone H3 phosphorylation and chromatin structure. J Biol Chem 2006; 282:4400-4407. [PMID: 17158874 DOI: 10.1074/jbc.m609041200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Histone H3 phosphorylation has been linked to various environmental stress responses and specific chromatin structure. The role of H3 phosphorylation in the osmotic stress response was investigated on the mouse mammary tumor virus (MMTV) promoter in different chromatin configurations. Hormone-dependent transcription from the MMTV promoter is repressed by osmotic stress when the promoter is integrated and has a normal chromatin structure. However, when the MMTV promoter is transiently transfected, the chromatin structure is less organized, and hormone induction is not affected by osmotic stress. On the integrated MMTV promoter, phosphorylation of histone H3 serine 10 and 28 increases in response to osmotic stress, but the transient promoter shows no change. Hormone-dependent glucocorticoid receptor binding is reduced on the repressed promoter, and elevated H3 phosphorylation is temporally correlated with maximal MMTV repression Additionally, the protein kinase C inhibitor rottlerin, but not other kinase inhibitors, blocks both histone H3 phosphorylation and osmotic repression of MMTV transcription. Glucocorticoid receptor binding is inversely correlated with H3 phosphorylation, suggesting that displacement of the glucocorticoid receptor from the promoter is due to H3 phosphorylation and is the mechanism for the osmotic repression of hormone-dependent transcription.
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Affiliation(s)
- Barbara A Burkhart
- Laboratory of Molecular Carcinogenesis, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Sarah B Kennett
- Laboratory of Molecular Carcinogenesis, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Trevor K Archer
- Laboratory of Molecular Carcinogenesis, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.
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Chen H, Shen WL, Wang XH, Chen HZ, Gu JZ, Fu J, Ni YF, Gao PJ, Zhu DL, Higashino H. Paradoxically enhanced heart tolerance to ischaemia in type 1 diabetes and role of increased osmolarity. Clin Exp Pharmacol Physiol 2006; 33:910-6. [PMID: 17002667 DOI: 10.1111/j.1440-1681.2006.04463.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
There is considerable controversy regarding the tolerance of diabetic hearts to ischaemia and the underlying mechanisms responsible for the increased heart tolerance to ischamia remain uncertain. In the present study, we observed, in vitro, type 1 diabetic heart responses to ischaemia and reperfusion at different degrees of hyperglycaemia. In addition, the possible role of increased osmolarity in cardioprotection due to hyperglycaemia was evaluated. Hearts from 3 week streptozocin-induced diabetic rats were isolated and perfused in a Langendorff apparatus and subjected to 30 min ischaemia and 30 min reperfusion. Cardiac function and the electrocardiogram were recorded. Myocardial content of osmolarity associated heat shock protein (hsp) 90, heme oxygenase (HO)-1 and anti-oxidant enzymes were determined in diabetic or hyperosmotic solution-perfused hearts using western blot. The hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG; 2 x 10(-7) mol/L) or the nitric oxide synthase (NOS) inhibitor Nomega-nitro-L-arginine methyl ester (1 x 10(-5) mol/L) was added to the perfusate to observe the effects of hsp90 inhibition and hsp90-associated endothelial NOS on ischaemic responses of diabetic hearts. Compared with normal control rats, diabetic hearts with severe hyperglycaemia (blood glucose > 20 mmol/L) showed markedly improved postischaemic heart function with fewer reperfusion arrhythmias. Mild hyperglycaemia (< 12 mmol/L) exhibited no significant cardioprotection. Elevated expression of hsp90 accompanied the enhanced resistance to ischaemia in diabetic hearts, which was abrogated by 17-AAG. In the presence of the NOS inhibitor, heart function was preserved, whereas reperfusion arrhythmias were increased in diabetes. Diabetic hearts also had markedly elevated HO-1 and catalase, with no significant change in superoxide dismutase. Hyperosmotic perfusion with glucose or mannitol also increased myocardial hsp90 and catalase. The present findings reveal that heart resistance to ischaemia is increased in short-term type 1 diabetes with severe hyperglycaemia. Elevated osmolarity caused by significant hyperglycaemia may contribute to the enhanced myocardial activity against oxidative injury during ischaemia and reperfusion.
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Affiliation(s)
- Hong Chen
- Department of Pharmacology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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63
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Chen Y, Schnetz MP, Irarrazabal CE, Shen RF, Williams CK, Burg MB, Ferraris JD. Proteomic identification of proteins associated with the osmoregulatory transcription factor TonEBP/OREBP: functional effects of Hsp90 and PARP-1. Am J Physiol Renal Physiol 2006; 292:F981-92. [PMID: 17148781 DOI: 10.1152/ajprenal.00493.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hypertonicity (e.g., high NaCl) activates the transcription factor tonicity-responsive enhancer/osmotic response element-binding protein (TonEBP/OREBP), increasing transcription of protective genes. In the present studies, by stably expressing amino acids 1-547 of TonEBP/OREBP in HEK 293 cells and immunoprecipitating it plus associated proteins from the nuclei of cells exposed to high NaCl, we identify 14 proteins that are physically associated with TonEBP/OREBP. The associated proteins fall into several classes: 1) DNA-dependent protein kinase, both its catalytic subunit and regulatory subunit, Ku86; 2) RNA helicases, namely RNA helicase A, nucleolar RNA helicase II/Gu, and DEAD-box RNA helicase p72; 3) small or heterogeneous nuclear ribonucleoproteins (snRNPs or hnRNPs), namely U5 snRNP-specific 116 kDa protein, U5 snRNP-specific 200 kDa protein, hnRNP U, hnRNP M, hnRNP K, and hnRNP F; 4) heat shock proteins, namely Hsp90beta and Hsc70; and 5) poly(ADP-ribose) polymerase-1 (PARP-1). We confirm identification of most of the proteins by Western analysis and also demonstrate by electrophoretic mobility-shift assay that they are present in the large complex that binds specifically along with TonEBP/OREBP to its cognate DNA element. In addition, we find that PARP-1 and Hsp90 modulate TonEBP/OREBP activity. PARP-1 expression reduces TonEBP/OREBP transcriptional activity and the activity of its transactivating domain. Hsp90 enhances those activities and sustains the increased abundance of TonEBP/OREBP protein in cells exposed to high NaCl.
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Affiliation(s)
- Ye Chen
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
Proteomic technologies are used with increasing frequency in the renal community. In this review, we highlight the use in renal research of a number of available techniques including two-dimensional gel electrophoresis, liquid chromatography/mass spectrometry, surface-enhanced laser desorption/ionization, capillary electrophoresis/mass spectrometry, and antibody and tissue arrays. These techniques have been used to identify proteins or changes in proteins specific to regions of the kidney or associated with renal diseases or toxicity. They have also been used to examine protein expression changes and posttranslational modifications of proteins during signaling. A number of studies have used proteomic methodologies to look for diagnostic biomarkers in body fluids. The rapid rate of development of the technologies along with the combination of classic physiological and biochemical techniques with proteomics will enable new discoveries.
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Affiliation(s)
- Michael G Janech
- Medical University of South Carolina, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29425-2220, USA
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65
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Sandoval JA, Eppstein AC, Hoelz DJ, Klein PJ, Linebarger JH, Turner KE, Rescorla FJ, Hickey RJ, Malkas LH, Schmidt CM. Proteomic Analysis of Neuroblastoma Subtypes in Response to Mitogen-Activated Protein Kinase Inhibition: Profiling Multiple Targets of Cancer Kinase Signaling. J Surg Res 2006; 134:61-7. [PMID: 16650873 DOI: 10.1016/j.jss.2006.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 02/03/2006] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Survival for high-risk neuroblastoma (NB) remains poor despite aggressive therapy. Novel therapies are vital for improving prognosis. We previously showed differential NB subtype sensitivity to p42/44 mitogen-activated protein kinase (ERK/MAPK) pathway inhibition. In this study, we investigated proteomic changes associated with resistance or sensitivity to MAPK kinase (MEK) inhibition in NB subtypes. MATERIALS AND METHODS SH-SY5Y (N-type), BE(2)-C (I-type), and SK-N-AS (S-type) were treated with MEK inhibitor U0126 (10 microM) for 1 and 24 h. Proteins were extracted from untreated and treated cells and analyzed for differential expression by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Selected polypeptides were extracted from the gel and identified by liquid chromatography-linked tandem mass spectrometry (LC-MS/MS). RESULTS We identified 15 proteins that were decreased by 2.5-fold between untreated and 1 h treated cells and subsequently up-regulated 5-fold after 24 h drug treatment. N-type NB (MEK-resistant) showed the least altered proteomic profile whereas the I-type (MEK-sensitive) and S-type NB (MEK-intermediate) generated significant protein changes. The majority of proteins identified were induced by stress. CONCLUSIONS Protein differences exist between MEK inhibitor-treated NB subtypes. Identified polypeptides all have roles in mediating cellular stress. These data suggest that inhibition of the ERK/MAPK in NB subtypes leads to an intracellular stress response. The most resistant NB cell line to MEK inhibitor treatment generated the least protective protein profile, whereas the intermediate and most sensitive NB cells produced the most stress response. These findings suggest stress related protein expression may be targeted in assessing a response to ERK/MAPK therapeutics.
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Affiliation(s)
- John A Sandoval
- Department of Surgery, Indiana University School of Medicine and JW Riley Hospital for Children, Indianapolis, Indiana 46202, USA
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Valkova N, Kültz D. Constitutive and inducible stress proteins dominate the proteome of the murine inner medullary collecting duct-3 (mIMCD3) cell line. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1007-20. [PMID: 16713411 DOI: 10.1016/j.bbapap.2006.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 03/13/2006] [Accepted: 03/16/2006] [Indexed: 11/29/2022]
Abstract
A proteome map of the most abundant proteins in the murine inner medullary collecting duct (mIMCD3) cell line was generated by 2-dimensional gel electrophoresis (2D-GE) combined with MALDI-TOF/TOF mass spectrometry. The 2-D model map identifies 77 distinct constitutive proteins and a total of 86 spots including isoforms. Protein identification was based on both peptide mass fingerprinting (MS) and peptide fragmentation (MS/MS) data. High confidence Mascot scores were obtained in the database search, due to the high quality and the number of MS/MS spectra which provided matching sequence information to the database. A functional classification of the identified proteins showed that a high proportion were stress proteins, such as heat shock proteins and proteins with anti-oxidant activity. Other proteins identified were involved in cytoskeletal maintenance, metabolism and energy generation, as well as in translation, transcription, RNA processing and other cell cycle processes. Exposure of the mIMCD3 cells to hyperosmotic stress using 600 mOsmol/kg NaCl or Urea or 700 mOsmol/kg NaCl-Urea (50:50) resulted in the greatest proteome upregulation in 700 mosM NaCl-Urea and the greatest downregulation in 600 mosM NaCl. Several proteins with molecular chaperone function were induced, such as alpha-B crystallin, two Hsp70 isoforms, the osmotic stress protein (Osp94), as well as aldose reductase. Additional isoforms of the translation elongation factors Eef2 and Eef1a1 were induced. Characterization of the phosphoproteome of mIMCD3 cells with a phosphoprotein-specific stain showed a significant proportion of the proteome was phosphorylated. Additionally, exposure of mIMCD3 cells to 600 mOsmol/kg NaCl hyperosmotic stress resulted in a 1.8-fold higher phosphorylation level of the most acidic isoform of the heat shock protein Hsp27 compared to its phosphorylation level under iso-osmotic conditions.
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Affiliation(s)
- Nelly Valkova
- Physiological Genomics Group, Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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67
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An Thieu V, Kirsch D, Flad T, Müller C, Spengler B. Direct Protein Identification from Nonspecific Peptide Pools by High-Accuracy MS Data Filtering. Angew Chem Int Ed Engl 2006; 45:3317-9. [PMID: 16619325 DOI: 10.1002/anie.200503787] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Vinh An Thieu
- Institut für Anorganische und Analytische Chemie, Justus Liebig Universität, Germany
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An Thieu V, Kirsch D, Flad T, Müller C, Spengler B. Direct Protein Identification from Nonspecific Peptide Pools by High-Accuracy MS Data Filtering. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hoffert JD, Pisitkun T, Wang G, Shen RF, Knepper MA. Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. Proc Natl Acad Sci U S A 2006; 103:7159-64. [PMID: 16641100 PMCID: PMC1459033 DOI: 10.1073/pnas.0600895103] [Citation(s) in RCA: 282] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation plays a key role in vasopressin signaling in the renal-collecting duct. Large-scale identification and quantification of phosphorylation events triggered by vasopressin is desirable to gain a comprehensive systems-level understanding of this process. We carried out phosphoproteomic analysis of rat inner medullary collecting duct cells by using a combination of phosphopeptide enrichment by immobilized metal affinity chromatography and phosphorylation site identification by liquid chromatography-mass spectrometry(n) neutral loss scanning. A total of 714 phosphorylation sites on 223 unique phosphoproteins were identified from inner medullary collecting duct samples treated short-term with either calyculin A or vasopressin. A number of proteins involved in cytoskeletal reorganization, vesicle trafficking, and transcriptional regulation were identified. Previously unidentified phosphorylation sites were found for membrane proteins essential to collecting duct physiology, including eight sites among aquaporin-2 (AQP2), aquaporin-4, and urea transporter isoforms A1 and A3. Through label-free quantification of phosphopeptides, we identified a number of proteins that significantly changed phosphorylation state in response to short-term vasopressin treatment: AQP2, Bclaf1, LRRC47, Rgl3, and SAFB2. In the presence of vasopressin, AQP2 monophosphorylated at S256 and diphosphorylated AQP2 (pS256/261) increased in abundance, whereas AQP2 monophosphorylated at S261 decreased, raising the possibility that both sites are involved in vasopressin-dependent AQP2 trafficking. This study reveals the practicality of liquid chromatography-mass spectrometry(n) neutral loss scanning for large-scale identification and quantification of protein phosphorylation in the analysis of cell signaling in a native mammalian system.
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Affiliation(s)
| | | | - Guanghui Wang
- National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Rong-Fong Shen
- National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Mark A. Knepper
- National Heart, Lung, and Blood Institute, Bethesda, MD 20892
- *To whom correspondence should be addressed at:
National Institutes of Health, Building 10, Room 6N260, 10 Center Drive, MSC 1603, Bethesda, MD 20892-1603.
E-mail:
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70
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Tomanek L. HENLE'S LOOP AND THE OSMOTIC STRESS PROTEOME. J Exp Biol 2006. [DOI: 10.1242/jeb.02160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Lars Tomanek
- California Polytechnic State University San Luis Obispo
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71
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Asif AR, Oellerich M, Amstrong VW, Riemenschneider B, Monod M, Reichard U. Proteome of Conidial Surface Associated Proteins ofAspergillusfumigatusReflecting Potential Vaccine Candidates and Allergens. J Proteome Res 2006; 5:954-62. [PMID: 16602703 DOI: 10.1021/pr0504586] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aspergillus fumigatus is a mold causing most of the invasive fungal lung infections in the immunocompromised host. In addition, the species is the causative agent of certain allergic diseases. Both in invasive and in allergic diseases, the conidial surface mediates the first contact with the human immune system. Thus, conidial surface proteins may be reasonable vaccine candidates as well as important allergens. To broaden the list of those antigens, intact viable Aspergillus conidia were extracted with mild alkaline buffer at pH 8.5 in the presence of a 1,3-beta-glucanase. The proteome of this fraction was separated by two- dimensional gel electrophoresis (2-DE) and analyzed by liquid chromatography coupled with tandem mass spectrometry. Altogether 26 different A. fumigatus proteins were identified, twelve of which contain a signal for secretion. Among these were the known major conidial surface protein rodlet A, one acid protease PEP2, one lipase, a putative disulfide isomerase and a putative fructose-1,6-biphosphatase. The known allergen Aspf 3 was identified among the proteins without a signal for secretion. On the basis of the recently annotated A. fumigatus genome (Nature 2005, 438, 1151-1156), proteome analysis is now a powerful tool to confirm expression of hypothetical proteins and, thereby to identify additional vaccine candidates and possible new allergens of this important fungal pathogen.
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Affiliation(s)
- Abdul R Asif
- Department of Clinical Chemistry, University Hospital of Göttingen, Germany
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Nishitani Y, Matsumoto H. Ethanol rapidly causes activation of JNK associated with ER stress under inhibition of ADH. FEBS Lett 2005; 580:9-14. [PMID: 16343492 DOI: 10.1016/j.febslet.2005.11.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 11/02/2005] [Accepted: 11/11/2005] [Indexed: 12/11/2022]
Abstract
Acute ethanol loading causes oxidative stress to activate cell-death signaling via c-Jun NH2-terminal kinase (JNK) in livers. JNK are stimulated under conditions of endoplasmic reticulum (ER) stress which causes programmed cell death. However, no remarked cell death was observed in acute ethanol intoxication. Akt, one of the cell survival protein kinases, may be activated under ethanol loading. The aim of this study was to estimate activation of JNK and ER stress, role of ethanol metabolism on the activation, and association of JNK with Akt under acute ethanol loading using the perfused rat liver system. Activation of JNK or Akt and association of JNK and Akt with JNK interacting protein 1 were estimated by immunoprecipitation and immunoblotting. Expression of 78 kDa glucose-regulated protein (GRP78) mRNA, a biomarker of ER stress, was detected by quantitative real-time RT-PCR. Activations of JNK and Akt were enhanced by co-treatment with ethanol and a classical inhibitor of alcohol dehydrogenase (ADH). Addition of an antioxidant reduced the activation of JNK. Ethanol loading with ADH inhibition causes down-regulation of GRP78 mRNA levels. Therefore, these findings suggest first revelation that inhibition of ethanol metabolism complicates oxidative and ER stresses produced by ethanol.
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Affiliation(s)
- Yoko Nishitani
- Department of Legal Medicine, Sapporo Medical University School of Medicine, S-1 W-17, Chuo-ku, Sapporo 060-8556, Japan
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