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Book ; Online ; Thesis: Massenspektrometrische Untersuchung posttranslationaler Modifikationen

Sarioglu, Hakan

Deamidierung als ubiquitäres Phänomen

2003

Author's details	vorgelegt von Hakan Sarioglu
Keywords	Posttranslationale Änderung ; Blutplasma ; Massenspektrometrie ; Proteomanalyse ; Deamidierung
Language	German
Size	Online-Ressource
Document type	Book ; Online ; Thesis
Thesis / German Habilitation thesis	Univ., Diss--München, 2003
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: Differential inhibition of Arabidopsis superoxide dismutases by peroxynitrite-mediated tyrosine nitration.

Holzmeister, Christian / Gaupels, Frank / Geerlof, Arie / Sarioglu, Hakan / Sattler, Michael / Durner, Jörg / Lindermayr, Christian

Journal of experimental botany

2015 Volume 66, Issue 3, Page(s) 989–999

Abstract: Despite the importance of superoxide dismutases (SODs) in the plant antioxidant defence system little is known about their regulation by post-translational modifications. Here, we investigated the in vitro effects of nitric oxide derivatives on the seven ...

Abstract	Despite the importance of superoxide dismutases (SODs) in the plant antioxidant defence system little is known about their regulation by post-translational modifications. Here, we investigated the in vitro effects of nitric oxide derivatives on the seven SOD isoforms of Arabidopsis thaliana. S-nitrosoglutathione, which causes S-nitrosylation of cysteine residues, did not influence SOD activities. By contrast, peroxynitrite inhibited the mitochondrial manganese SOD1 (MSD1), peroxisomal copper/zinc SOD3 (CSD3), and chloroplastic iron SOD3 (FSD3), but no other SODs. MSD1 was inhibited by up to 90% but CSD3 and FSD3 only by a maximum of 30%. Down-regulation of these SOD isoforms correlated with tyrosine (Tyr) nitration and both could be prevented by the peroxynitrite scavenger urate. Site-directed mutagenesis revealed that-amongst the 10 Tyr residues present in MSD1-Tyr63 was the main target responsible for nitration and inactivation of the enzyme. Tyr63 is located nearby the active centre at a distance of only 5.26 Å indicating that nitration could affect accessibility of the substrate binding pocket. The corresponding Tyr34 of human manganese SOD is also nitrated, suggesting that this might be an evolutionarily conserved mechanism for regulation of manganese SODs.
MeSH term(s)	Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Peroxynitrous Acid/metabolism ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Sequence Alignment ; Superoxide Dismutase/chemistry ; Superoxide Dismutase/genetics ; Superoxide Dismutase/metabolism ; Tyrosine/metabolism
Chemical Substances	Plant Proteins ; Peroxynitrous Acid (14691-52-2) ; Tyrosine (42HK56048U) ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2015-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/eru458
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online ; Thesis: Massenspektrometrische Untersuchung posttranslationaler Modifikationen

Sarioglu, Hakan [Verfasser]

Deamidierung als ubiquitäres Phänomen

2003

Author's details	vorgelegt von Hakan Sarioglu
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: The Epoxyeicosatrienoic Acid Pathway Enhances Hepatic Insulin Signaling and is Repressed in Insulin-Resistant Mouse Liver.

Schäfer, Alexander / Neschen, Susanne / Kahle, Melanie / Sarioglu, Hakan / Gaisbauer, Tobias / Imhof, Axel / Adamski, Jerzy / Hauck, Stefanie M / Ueffing, Marius

Molecular & cellular proteomics : MCP

2015 Volume 14, Issue 10, Page(s) 2764–2774

Abstract: Although it is widely accepted that ectopic lipid accumulation in the liver is associated with hepatic insulin resistance, the underlying molecular mechanisms have not been well characterized.Here we employed time resolved quantitative proteomic ... ...

Abstract	Although it is widely accepted that ectopic lipid accumulation in the liver is associated with hepatic insulin resistance, the underlying molecular mechanisms have not been well characterized.Here we employed time resolved quantitative proteomic profiling of mice fed a high fat diet to determine which pathways were affected during the transition of the liver to an insulin-resistant state. We identified several metabolic pathways underlying altered protein expression. In order to test the functional impact of a critical subset of these alterations, we focused on the epoxyeicosatrienoic acid (EET) eicosanoid pathway, whose deregulation coincided with the onset of hepatic insulin resistance. These results suggested that EETs may be positive modulators of hepatic insulin signaling. Analyzing EET activity in primary hepatocytes, we found that EETs enhance insulin signaling on the level of Akt. In contrast, EETs did not influence insulin receptor or insulin receptor substrate-1 phosphorylation. This effect was mediated through the eicosanoids, as overexpression of the deregulated enzymes in absence of arachidonic acid had no impact on insulin signaling. The stimulation of insulin signaling by EETs and depression of the pathway in insulin resistant liver suggest a likely role in hepatic insulin resistance. Our findings support therapeutic potential for inhibiting EET degradation.
MeSH term(s)	Animals ; Cell Line ; Diet, High-Fat ; Eicosanoids/metabolism ; Hepatocytes/metabolism ; Insulin/metabolism ; Insulin Resistance ; Liver/metabolism ; Male ; Mice ; Mice, Inbred C3H ; Proteomics ; Safflower Oil ; Signal Transduction
Chemical Substances	Eicosanoids ; Insulin ; Safflower Oil (8001-23-8)
Language	English
Publishing date	2015-06-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.M115.049064
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Article ; Online: Quantitative and integrated proteome and microRNA analysis of endothelial replicative senescence.

Yentrapalli, Ramesh / Azimzadeh, Omid / Kraemer, Anne / Malinowsky, Katharina / Sarioglu, Hakan / Becker, Karl-Friedrich / Atkinson, Michael J / Moertl, Simone / Tapio, Soile

Journal of proteomics

2015 Volume 126, Page(s) 12–23

Abstract: Age-related changes in vascular functioning are a harbinger of cardiovascular disease but the biological mechanisms during the progression of endothelial senescence have not been studied. We investigated alterations in the proteome and miRNA profiles in ... ...

Abstract	Age-related changes in vascular functioning are a harbinger of cardiovascular disease but the biological mechanisms during the progression of endothelial senescence have not been studied. We investigated alterations in the proteome and miRNA profiles in the course of replicative senescence using primary human umbilical vein endothelial cells as an in vitro vascular model. Quantitative proteomic profiling from early growth stage to senescence was performed by isotope-coded protein label coupled to LC-ESI-MS/MS analysis. Some proteins consistently changed their expression during the senescence whereas others appeared as deregulated only during the late senescence. The latter was accompanied by alterations in morphology of senescent endothelial cells. MicroRNA expression profiling revealed transient changes in the level of miR-16-5p, miR-28-3p and miR-886-5p in the early senescence, decrease in the level of miR-106b-3p at the late stage, and continuous changes in the expression of miR-181a-5p and miR-376a-3p during the whole senescence process. Integrating data on proteomic and microRNA changes indicated potential crosstalk between specific proteins and non-coding RNAs in the regulation of metabolism, cell cycle progression and cytoskeletal organization in the endothelial senescence. The knowledge of molecular targets that change during the senescence can ultimately contribute to a better understanding and prevention of age-related vascular diseases.
MeSH term(s)	Cellular Senescence/physiology ; Human Umbilical Vein Endothelial Cells/cytology ; Human Umbilical Vein Endothelial Cells/metabolism ; Humans ; MicroRNAs/metabolism ; Proteome/metabolism ; Proteomics
Chemical Substances	MicroRNAs ; Proteome
Language	English
Publishing date	2015-08-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2015.05.023
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Article ; Online: Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin.

Fröhlich, Andreas / Gaupels, Frank / Sarioglu, Hakan / Holzmeister, Christian / Spannagl, Manuel / Durner, Jörg / Lindermayr, Christian

Plant physiology

2012 Volume 159, Issue 3, Page(s) 902–914

Abstract: The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic ... ...

Abstract	The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome.
MeSH term(s)	Arabidopsis/metabolism ; Arabidopsis/microbiology ; Arabidopsis Proteins/metabolism ; Chemical Fractionation ; Chromatography, Liquid ; Combinatorial Chemistry Techniques ; Cucurbita/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Hydrogen-Ion Concentration ; Mass Spectrometry ; Peptide Library ; Phloem/metabolism ; Plant Extracts/metabolism ; Plant Exudates/metabolism ; Plant Leaves/metabolism ; Plant Leaves/microbiology ; Pseudomonas syringae/physiology
Chemical Substances	Arabidopsis Proteins ; Peptide Library ; Plant Extracts ; Plant Exudates
Language	English
Publishing date	2012-05-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.112.198077
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Integrative Proteomics and Targeted Transcriptomics Analyses in Cardiac Endothelial Cells Unravel Mechanisms of Long-Term Radiation-Induced Vascular Dysfunction

Azimzadeh, Omid / Atkinson Michael J / Bakshi Mayur V / Janik Dirk / Merl-Pham Juliane / Multhoff Gabriele / Sarioglu Hakan / Sievert Wolfgang / Tapio Soile / Ueffing Marius / Yentrapalli Ramesh

Journal of Proteome Research. 2015 Feb. 06, v. 14, no. 2

2015

Abstract: Epidemiological data from radiotherapy patients show the damaging effect of ionizing radiation on heart and vasculature. The endothelium is the main target of radiation damage and contributes essentially to the development of cardiac injury. However, the ...

Abstract	Epidemiological data from radiotherapy patients show the damaging effect of ionizing radiation on heart and vasculature. The endothelium is the main target of radiation damage and contributes essentially to the development of cardiac injury. However, the molecular mechanisms behind the radiation-induced endothelial dysfunction are not fully understood. In the present study, 10-week-old C57Bl/6 mice received local X-ray heart doses of 8 or 16 Gy and were sacrificed after 16 weeks; the controls were sham-irradiated. The cardiac microvascular endothelial cells were isolated from the heart tissue using streptavidin-CD31-coated microbeads. The cells were lysed and proteins were labeled with duplex isotope-coded protein label methodology for quantification. All samples were analyzed by LCâESIâMS/MS and Proteome Discoverer software. The proteomics data were further studied by bioinformatics tools and validated by targeted transcriptomics, immunoblotting, immunohistochemistry, and serum profiling. Radiation-induced endothelial dysfunction was characterized by impaired energy metabolism and perturbation of the insulin/IGF-PI3K-Akt signaling pathway. The data also strongly suggested premature endothelial senescence, increased oxidative stress, decreased NO availability, and enhanced inflammation as main causes of radiation-induced long-term vascular dysfunction. Detailed data on molecular mechanisms of radiation-induced vascular injury as compiled here are essential in developing radiotherapy strategies that minimize cardiovascular complications.
Keywords	bioinformatics ; blood serum ; computer software ; endothelial cells ; endothelium ; energy metabolism ; heart ; immunoblotting ; immunohistochemistry ; inflammation ; mice ; microbeads ; nitric oxide ; oxidative stress ; patients ; proteins ; proteome ; proteomics ; radiotherapy ; signal transduction ; transcriptomics ; X-radiation
Language	English
Dates of publication	2015-0206
Size	p. 1203-1219.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Fpr501141b
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Quantitative and integrated proteome and microRNA analysis of endothelial replicative senescence

Yentrapalli, Ramesh / Azimzadeh, Omid / Kraemer, Anne / Malinowsky, Katharina / Sarioglu, Hakan / Becker, Karl Friedrich / Atkinson, Michael J. / Moertl, Simone / Tapio, Soile

Journal of proteomics. 2015 Aug. 03, v. 126 p.12-23

2015

Abstract	Age-related changes in vascular functioning are a harbinger of cardiovascular disease but the biological mechanisms during the progression of endothelial senescence have not been studied. We investigated alterations in the proteome and miRNA profiles in the course of replicative senescence using primary human umbilical vein endothelial cells as an in vitro vascular model. Quantitative proteomic profiling from early growth stage to senescence was performed by isotope-coded protein label coupled to LC-ESI-MS/MS analysis. Some proteins consistently changed their expression during the senescence whereas others appeared as deregulated only during the late senescence. The latter was accompanied by alterations in morphology of senescent endothelial cells. MicroRNA expression profiling revealed transient changes in the level of miR-16-5p, miR-28-3p and miR-886-5p in the early senescence, decrease in the level of miR-106b-3p at the late stage, and continuous changes in the expression of miR-181a-5p and miR-376a-3p during the whole senescence process. Integrating data on proteomic and microRNA changes indicated potential crosstalk between specific proteins and non-coding RNAs in the regulation of metabolism, cell cycle progression and cytoskeletal organization in the endothelial senescence. The knowledge of molecular targets that change during the senescence can ultimately contribute to a better understanding and prevention of age-related vascular diseases.
Keywords	cell cycle ; cell senescence ; cytoskeleton ; developmental stages ; human umbilical vein endothelial cells ; metabolism ; microRNA ; models ; non-coding RNA ; proteins ; proteome ; proteomics ; vascular diseases ; HUVEC ; IPA ; ICPL ; ESI ; LC ; MS/MS ; miRNA ; mRNA ; MVS ; PCR ; RPPA ; Endothelial cell ; Cellular senescence ; Proteomics
Language	English
Dates of publication	2015-0803
Size	p. 12-23.
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2015.05.023
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Proteomic analysis of defense response of wildtype Arabidopsis thaliana and plants with impaired NO- homeostasis.

Holzmeister, Christian / Fröhlich, Andreas / Sarioglu, Hakan / Bauer, Norbert / Durner, Jörg / Lindermayr, Christian

Proteomics

2011 Volume 11, Issue 9, Page(s) 1664–1683

Abstract: In recent years, nitric oxide (NO) has been recognized as a signalling molecule of plants, being involved in diverse processes like germination, root growth, stomatal closing, and responses to various stresses. A mechanism of how NO can regulate ... ...

Abstract	In recent years, nitric oxide (NO) has been recognized as a signalling molecule of plants, being involved in diverse processes like germination, root growth, stomatal closing, and responses to various stresses. A mechanism of how NO can regulate physiological processes is the modulation of cysteine residues of proteins (S-nitrosylation) by S-nitrosoglutathione (GSNO), a physiological NO donor. The concentration of GSNO and the level of S-nitrosylated proteins are regulated by GSNO reductase, which seems to play a major role in NO signalling. To investigate the importance of NO in plant defense response, we performed a proteomic analysis of Arabidopsis wildtype and GSNO-reductase knock-out plants infected with both the avirulent and virulent pathogen strains of Pseudomonas syringae. Using 2-D DIGE technology in combination with MS, we identified proteins, which are differentially accumulated during the infection process. We observed that both lines were more resistant to avirulent infections than to virulent infections mainly due to the accumulation of stress-, redox-, and defense-related proteins. Interestingly, after virulent infections, we also observed accumulation of defense-related proteins, but no or low accumulation of stress- and redox-related proteins, respectively. In summary, we present here the first detailed proteomic analysis of plant defense response.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis/microbiology ; Arabidopsis Proteins/analysis ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Glutathione Reductase/genetics ; Homeostasis ; Host-Pathogen Interactions/genetics ; Mutation ; Nitric Oxide/metabolism ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Proteome/analysis ; Proteome/metabolism ; Proteomics/methods ; Pseudomonas syringae/pathogenicity ; Pseudomonas syringae/physiology ; Signal Transduction ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Virulence
Chemical Substances	Arabidopsis Proteins ; Proteome ; Nitric Oxide (31C4KY9ESH) ; Glutathione Reductase (EC 1.8.1.7) ; S-nitrosoglutathione reductase, Arabidopsis (EC 1.8.1.7)
Language	English
Publishing date	2011-05
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201000652
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Cell survival following radiation exposure requires miR-525-3p mediated suppression of ARRB1 and TXN1.

Kraemer, Anne / Barjaktarovic, Zarko / Sarioglu, Hakan / Winkler, Klaudia / Eckardt-Schupp, Friederike / Tapio, Soile / Atkinson, Michael J / Moertl, Simone

PloS one

2013 Volume 8, Issue 10, Page(s) e77484

Abstract: Background: microRNAs (miRNAs) are non-coding RNAs that alter the stability and translation efficiency of messenger RNAs. Ionizing radiation (IR) induces rapid and selective changes in miRNA expression. Depletion of the miRNA processing enzymes Dicer or ...

Abstract	Background: microRNAs (miRNAs) are non-coding RNAs that alter the stability and translation efficiency of messenger RNAs. Ionizing radiation (IR) induces rapid and selective changes in miRNA expression. Depletion of the miRNA processing enzymes Dicer or Ago2 reduces the capacity of cells to survive radiation exposure. Elucidation of critical radiation-regulated miRNAs and their target proteins offers a promising approach to identify new targets to increase the therapeutic effectiveness of the radiation treatment of cancer. Principal findings: Expression of miR-525-3p is rapidly up-regulated in response to radiation. Manipulation of miR-525-3p expression in irradiated cells confirmed that this miRNA mediates the radiosensitivity of a variety of non-transformed (RPE, HUVEC) and tumor-derived cell lines (HeLa, U2-Os, EA.hy926) cell lines. Thus, anti-miR-525-3p mediated inhibition of the increase in miR-525-3p elevated radiosensitivity, while overexpression of precursor miR-525-3p conferred radioresistance. Using a proteomic approach we identified 21 radiation-regulated proteins, of which 14 were found to be candidate targets for miR-525-3p-mediated repression. Luciferase reporter assays confirmed that nine of these were indeed direct targets of miR-525-3p repression. Individual analysis of these direct targets by RNAi-mediated knockdown established that ARRB1, TXN1 and HSPA9 are essential miR-525-3p-dependent regulators of radiation sensitivity. Conclusion: The transient up-regulation of miR-525-3p, and the resultant repression of its direct targets ARRB1, TXN1 and HSPA9, is required for cell survival following irradiation. The conserved function of miR-525-3p across several cell types makes this microRNA pathway a promising target for modifying the efficacy of radiotherapy.
MeSH term(s)	Arrestins/genetics ; Arrestins/metabolism ; Base Pairing ; Base Sequence ; Cell Line ; Cell Survival/genetics ; Cell Survival/radiation effects ; Dose-Response Relationship, Radiation ; Gene Expression Profiling ; Gene Expression Regulation/radiation effects ; Gene Regulatory Networks ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Molecular Sequence Annotation ; Proteome ; Proteomics ; RNA Interference ; Radiation Tolerance/genetics ; Signal Transduction ; Thioredoxins/chemistry ; Thioredoxins/genetics ; Thioredoxins/metabolism ; beta-Arrestin 1 ; beta-Arrestins
Chemical Substances	ARRB1 protein, human ; Arrestins ; HSP70 Heat-Shock Proteins ; HSPA9 protein, human ; MIRN525 microRNA, human ; MicroRNAs ; Mitochondrial Proteins ; Proteome ; TXN protein, human ; beta-Arrestin 1 ; beta-Arrestins ; Thioredoxins (52500-60-4)
Language	English
Publishing date	2013-10-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0077484
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