1
|
Rathner A, Rathner P, Friedrich A, Wießner M, Kitzler CM, Schernthaner J, Karl T, Krauß J, Lottspeich F, Mewes W, Hintner H, Bauer JW, Breitenbach M, Müller N, Breitenbach-Koller H, von Hagen J. Drug Development for Target Ribosomal Protein rpL35/uL29 for Repair of LAMB3R635X in Rare Skin Disease Epidermolysis Bullosa. Skin Pharmacol Physiol 2021; 34:167-182. [PMID: 33823521 DOI: 10.1159/000513260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/22/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Epidermolysis bullosa (EB) describes a family of rare genetic blistering skin disorders. Various subtypes are clinically and genetically heterogeneous, and a lethal postpartum form of EB is the generalized severe junctional EB (gs-JEB). gs-JEB is mainly caused by premature termination codon (PTC) mutations in the skin anchor protein LAMB3 (laminin subunit beta-3) gene. The ribosome in majority of translational reads of LAMB3PTC mRNA aborts protein synthesis at the PTC signal, with production of a truncated, nonfunctional protein. This leaves an endogenous readthrough mechanism needed for production of functional full-length Lamb3 protein albeit at insufficient levels. Here, we report on the development of drugs targeting ribosomal protein L35 (rpL35), a ribosomal modifier for customized increase in production of full-length Lamb3 protein from a LAMB3PTC mRNA. METHODS Molecular docking studies were employed to identify small molecules binding to human rpL35. Molecular determinants of small molecule binding to rpL35 were further characterized by titration of the protein with these ligands as monitored by nuclear magnetic resonance (NMR) spectroscopy in solution. Changes in NMR chemical shifts were used to map the docking sites for small molecules onto the 3D structure of the rpL35. RESULTS Molecular docking studies identified 2 FDA-approved drugs, atazanavir and artesunate, as candidate small-molecule binders of rpL35. Molecular interaction studies predicted several binding clusters for both compounds scattered throughout the rpL35 structure. NMR titration studies identified the amino acids participating in the ligand interaction. Combining docking predictions for atazanavir and artesunate with rpL35 and NMR analysis of rpL35 ligand interaction, one binding cluster located near the N-terminus of rpL35 was identified. In this region, the nonidentical binding sites for atazanavir and artesunate overlap and are accessible when rpL35 is integrated in its natural ribosomal environment. CONCLUSION Atazanavir and artesunate were identified as candidate compounds binding to ribosomal protein rpL35 and may now be tested for their potential to trigger a rpL35 ribosomal switch to increase production of full-length Lamb3 protein from a LAMB3PTC mRNA for targeted systemic therapy in treating gs-JEB.
Collapse
Affiliation(s)
- Adriana Rathner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Petr Rathner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
- Institute of Inorganic Chemistry, Johannes Kepler University, Linz, Austria
| | - Andreas Friedrich
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Michael Wießner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
- Department of Allergology and Dermatology, University Hospital Salzburg, Salzburg, Austria
| | | | - Jan Schernthaner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Thomas Karl
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Jan Krauß
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Werner Mewes
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Helmut Hintner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
- Department of Allergology and Dermatology, University Hospital Salzburg, Salzburg, Austria
| | - Johann W Bauer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
- Department of Allergology and Dermatology, University Hospital Salzburg, Salzburg, Austria
| | | | - Norbert Müller
- Institute of Inorganic Chemistry, Johannes Kepler University, Linz, Austria
- Institute of Organic Chemistry, Johannes Kepler University, Linz, Austria
- Faculty of Natural Sciences, University of South Bohemia, Ceske Budejovice, Czechia
| | | | - Jörg von Hagen
- Department of Life Science Engineering, Technische Hochschule Mittelhessen, Gießen, Germany
| |
Collapse
|
2
|
|
3
|
Affiliation(s)
- Agnes Henschen
- The Max-Planck-Institut für Biochemie, Martinsried bei München, West-Germany
| | | | | | - Renate Warbinek
- The Max-Planck-Institut für Biochemie, Martinsried bei München, West-Germany
| |
Collapse
|
4
|
Affiliation(s)
| | | | - Agnes Henschen
- The Max-Planck-Institut für Biochemie, Martinsried bei München, West-Germany
| |
Collapse
|
5
|
Affiliation(s)
| | - Louise C Serpell
- b School of Life Sciences , University of Sussex , Brighton , UK
| | | | - Mitsuyasu Toyoda
- d Department of Surgical Pathology , Tokyo Medical College Hospital Nishishinjuku , Sinjuku-ku , Tokyo , Japan
| |
Collapse
|
6
|
Evaristo GP, Pinkse MW, Chen T, Wang L, Mohammed S, Heck AJ, Mathes I, Lottspeich F, Shaw C, Albar JP, Verhaert PD. De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
7
|
Henschen A, Lottspeich F, Töpfer-Petersen E, Warbinek R. On the primary structure of fibrinogen. Bibl Haematol 2015; 44:106-13. [PMID: 617774 DOI: 10.1159/000402158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
8
|
Bárcena-Uribarri I, Thein M, Barbot M, Sans-Serramitjana E, Bonde M, Mentele R, Lottspeich F, Bergström S, Benz R. Study of the protein complex, pore diameter, and pore-forming activity of the Borrelia burgdorferi P13 porin. J Biol Chem 2014; 289:18614-24. [PMID: 24825899 DOI: 10.1074/jbc.m113.539528] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P13 is one of the major outer membrane proteins of Borrelia burgdorferi. Previous studies described P13 as a porin. In the present study some structure and function aspects of P13 were studied. P13 showed according to lipid bilayer studies a channel-forming activity of 0.6 nanosiemens in 1 m KCl. Single channel and selectivity measurements demonstrated that P13 had no preference for either cations or anions and showed no voltage-gating up to ±100 mV. Blue native polyacrylamide gel electrophoresis was used to isolate and characterize the P13 protein complex in its native state. The complex had a high molecular mass of about 300 kDa and was only composed of P13 monomers. The channel size was investigated using non-electrolytes revealing an apparent diameter of about 1.4 nm with a 400-Da molecular mass cut-off. Multichannel titrations with different substrates reinforced the idea that P13 forms a general diffusion channel. The identity of P13 within the complex was confirmed by second dimension SDS-PAGE, Western blotting, mass spectrometry, and the use of a p13 deletion mutant strain. The results suggested that P13 is the protein responsible for the 0.6-nanosiemens pore-forming activity in the outer membrane of B. burgdorferi.
Collapse
Affiliation(s)
- Iván Bárcena-Uribarri
- From the Rudolf-Virchow-Center, Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany, School of Engineering and Science, Jacobs University Bremen, Campusring 1, D-28759 Bremen, Germany,
| | - Marcus Thein
- From the Rudolf-Virchow-Center, Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany
| | - Mariam Barbot
- From the Rudolf-Virchow-Center, Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany
| | - Eulalia Sans-Serramitjana
- From the Rudolf-Virchow-Center, Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany
| | - Mari Bonde
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden, and
| | - Reinhard Mentele
- Max-Planck Institute of Biochemistry, Protein Analysis Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Friedrich Lottspeich
- Max-Planck Institute of Biochemistry, Protein Analysis Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Sven Bergström
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden, and
| | - Roland Benz
- From the Rudolf-Virchow-Center, Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany, School of Engineering and Science, Jacobs University Bremen, Campusring 1, D-28759 Bremen, Germany
| |
Collapse
|
9
|
Hierl G, Höwing T, Isono E, Lottspeich F, Gietl C. Ex vivo processing for maturation of Arabidopsis KDEL-tailed cysteine endopeptidase 2 (AtCEP2) pro-enzyme and its storage in endoplasmic reticulum derived organelles. Plant Mol Biol 2014; 84:605-20. [PMID: 24287716 PMCID: PMC3950626 DOI: 10.1007/s11103-013-0157-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/19/2013] [Indexed: 05/24/2023]
Abstract
Ricinosomes are specialized ER-derived organelles that store the inactive pro-forms of KDEL-tailed cysteine endopeptidases (KDEL-CysEP) associated with programmed cell death (PCD). The Arabidopsis genome encodes three KDEL-CysEP (AtCEP1, AtCEP2, and AtCEP3) that are differentially expressed in vegetative and generative tissues undergoing PCD. These Arabidopsis proteases have not been characterized at a biochemical level, nor have they been localized intracellularly. In this study, we characterized AtCEP2. A 3xHA-mCherry-AtCEP2 gene fusion including pro-peptide and KDEL targeting sequences expressed under control of the endogenous promoter enabled us to isolate AtCEP2 "ex vivo". The purified protein was shown to be activated in a pH-dependent manner. After activation, however, protease activity was pH-independent. Analysis of substrate specificity showed that AtCEP2 accepts proline near the cleavage site, which is a rare feature specific for KDEL-CysEPs. mCherry-AtCEP2 was detected in the epidermal layers of leaves, hypocotyls and roots; in the root, it was predominantly found in the elongation zone and root cap. Co-localization with an ER membrane marker showed that mCherry-AtCEP2 was stored in two different types of ER-derived organelles: 10 μm long spindle shaped organelles as well as round vesicles with a diameter of approximately 1 μm. The long organelles appear to be ER bodies, which are found specifically in Brassicacae. The round vesicles strongly resemble the ricinosomes first described in castor bean. This study provides a first evidence for the existence of ricinosomes in Arabidopsis, and may open up new avenues of research in the field of PCD and developmental tissue remodeling.
Collapse
Affiliation(s)
- Georg Hierl
- Center of Life and Food Sciences Weihenstephan, Lehrstuhl fuer Botanik, Technische Universitaet Muenchen, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Timo Höwing
- Center of Life and Food Sciences Weihenstephan, Lehrstuhl fuer Botanik, Technische Universitaet Muenchen, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Erika Isono
- Center of Life and Food Sciences Weihenstephan, Department of Plant Systems Biology, Technische Universitaet Muenchen, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Friedrich Lottspeich
- Max Planck Institute of Biochemistry, Protein Analysis, 82152 Martinsried, Germany
| | - Christine Gietl
- Center of Life and Food Sciences Weihenstephan, Lehrstuhl fuer Botanik, Technische Universitaet Muenchen, Emil-Ramann-Str. 4, 85350 Freising, Germany
| |
Collapse
|
10
|
Grimm R, Eckerskorn C, Lottspeich F, Schäfer E. Rapid Phosphorylation of H3 Histone in Isolated Nuclei of Barley (Hordeum vulgareL.). ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1991.tb00196.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Chiocchetti AG, Haslinger D, Boesch M, Karl T, Wiemann S, Freitag CM, Poustka F, Scheibe B, Bauer JW, Hintner H, Breitenbach M, Kellermann J, Lottspeich F, Klauck SM, Breitenbach-Koller L. Protein signatures of oxidative stress response in a patient specific cell line model for autism. Mol Autism 2014; 5:10. [PMID: 24512814 PMCID: PMC3931328 DOI: 10.1186/2040-2392-5-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/23/2014] [Indexed: 12/26/2022] Open
Abstract
Background Known genetic variants can account for 10% to 20% of all cases with autism spectrum disorders (ASD). Overlapping cellular pathomechanisms common to neurons of the central nervous system (CNS) and in tissues of peripheral organs, such as immune dysregulation, oxidative stress and dysfunctions in mitochondrial and protein synthesis metabolism, were suggested to support the wide spectrum of ASD on unifying disease phenotype. Here, we studied in patient-derived lymphoblastoid cell lines (LCLs) how an ASD-specific mutation in ribosomal protein RPL10 (RPL10[H213Q]) generates a distinct protein signature. We compared the RPL10[H213Q] expression pattern to expression patterns derived from unrelated ASD patients without RPL10[H213Q] mutation. In addition, a yeast rpl10 deficiency model served in a proof-of-principle study to test for alterations in protein patterns in response to oxidative stress. Methods Protein extracts of LCLs from patients, relatives and controls, as well as diploid yeast cells hemizygous for rpl10, were subjected to two-dimensional gel electrophoresis and differentially regulated spots were identified by mass spectrometry. Subsequently, Gene Ontology database (GO)-term enrichment and network analysis was performed to map the identified proteins into cellular pathways. Results The protein signature generated by RPL10[H213Q] is a functionally related subset of the ASD-specific protein signature, sharing redox-sensitive elements in energy-, protein- and redox-metabolism. In yeast, rpl10 deficiency generates a specific protein signature, harboring components of pathways identified in both the RPL10[H213Q] subjects’ and the ASD patients’ set. Importantly, the rpl10 deficiency signature is a subset of the signature resulting from response of wild-type yeast to oxidative stress. Conclusions Redox-sensitive protein signatures mapping into cellular pathways with pathophysiology in ASD have been identified in both LCLs carrying the ASD-specific mutation RPL10[H213Q] and LCLs from ASD patients without this mutation. At pathway levels, this redox-sensitive protein signature has also been identified in a yeast rpl10 deficiency and an oxidative stress model. These observations point to a common molecular pathomechanism in ASD, characterized in our study by dysregulation of redox balance. Importantly, this can be triggered by the known ASD-RPL10[H213Q] mutation or by yet unknown mutations of the ASD cohort that act upstream of RPL10 in differential expression of redox-sensitive proteins.
Collapse
Affiliation(s)
- Andreas G Chiocchetti
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.,Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Denise Haslinger
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria.,Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Maximilian Boesch
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Thomas Karl
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University, Deutschordenstr. 50, 60528 Frankfurt am Main, Germany
| | - Burghardt Scheibe
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Johann W Bauer
- Department of Dermatology, General Hospital Salzburg/PMU, Müllner-Hauptstr. 48, 5020 Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology, General Hospital Salzburg/PMU, Müllner-Hauptstr. 48, 5020 Salzburg, Austria
| | - Michael Breitenbach
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Josef Kellermann
- Max-Planck-Institute of Biochemistry, Protein Analysis Group, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedrich Lottspeich
- Max-Planck-Institute of Biochemistry, Protein Analysis Group, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Lore Breitenbach-Koller
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| |
Collapse
|
12
|
Brunner A, Kellermann J, Lottspeich F. A practical guide to the ICPL_ESIQuant software for ICPL-based quantitative proteomics. Biochim Biophys Acta 2013; 1844:21-8. [PMID: 23454610 DOI: 10.1016/j.bbapap.2013.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/27/2012] [Accepted: 02/13/2013] [Indexed: 11/29/2022]
Abstract
ICPL_ESIQuant is a proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. It is able to process mass spectrometric data from various vendors and implements results from the Mascot search engine to generate protein and peptide result tables. This protocol briefly introduces ICPL_ESIQuant and presents a detailed step by step tutorial, how to use the software with MS datasets obtained from ICPL duplex, triplex and quadruplex experiments. Requiring MS raw data in .mzXML file format and Mascot search results in .dat format as input, ICPL_ESIQuant reliably quantifies ICPL labeled proteins and provides additional information about all detected, sequenced and identified features in the sample. The software supports both the shotgun and the directed proteomics strategy, enabling the user to apply mass inclusion lists for identifying peptides not fragmented in the first MS cycle. The software together with a test dataset is freely available under http://sourceforge.net/projects/icplquant/. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
Collapse
Affiliation(s)
- Achim Brunner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| | | | | |
Collapse
|
13
|
F. Moin S, Rainer M, Waheed H, Stasyk T, A. Huber L, Lottspeich F, K. Bonn G. Purification and Characterization of a Phospholipase A2 and Identification of a kappa Bungarotoxin from Bungarus sindanus sindanus (Sindhi Krait) Snake Venom. CURR ANAL CHEM 2011. [DOI: 10.2174/1573411011107030176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Vögtle FN, Prinz C, Kellermann J, Lottspeich F, Pfanner N, Meisinger C. Mitochondrial protein turnover: role of the precursor intermediate peptidase Oct1 in protein stabilization. Mol Biol Cell 2011; 22:2135-43. [PMID: 21525245 PMCID: PMC3128517 DOI: 10.1091/mbc.e11-02-0169] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/19/2011] [Accepted: 04/21/2011] [Indexed: 11/11/2022] Open
Abstract
Most mitochondrial proteins are encoded in the nucleus as precursor proteins and carry N-terminal presequences for import into the organelle. The vast majority of presequences are proteolytically removed by the mitochondrial processing peptidase (MPP) localized in the matrix. A subset of precursors with a characteristic amino acid motif is additionally processed by the mitochondrial intermediate peptidase (MIP) octapeptidyl aminopeptidase 1 (Oct1), which removes an octapeptide from the N-terminus of the precursor intermediate. However, the function of this second cleavage step is elusive. In this paper, we report the identification of a novel Oct1 substrate protein with an unusual cleavage motif. Inspection of the Oct1 substrates revealed that the N-termini of the intermediates typically carry a destabilizing amino acid residue according to the N-end rule of protein degradation, whereas mature proteins carry stabilizing N-terminal residues. We compared the stability of intermediate and mature forms of Oct1 substrate proteins in organello and in vivo and found that Oct1 cleavage increases the half-life of its substrate proteins, most likely by removing destabilizing amino acids at the intermediate's N-terminus. Thus Oct1 converts unstable precursor intermediates generated by MPP into stable mature proteins.
Collapse
Affiliation(s)
- F.-Nora Vögtle
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
- Trinationales Graduiertenkolleg 1478, Universität Freiburg, 79104 Freiburg, Germany
- Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Claudia Prinz
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Josef Kellermann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
- BIOSS, Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Chris Meisinger
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
- BIOSS, Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
15
|
Keidel EM, Dosch D, Brunner A, Kellermann J, Lottspeich F. Evaluation of protein loading techniques and improved separation in OFFGEL isoelectric focusing. Electrophoresis 2011; 32:1659-66. [PMID: 21563181 DOI: 10.1002/elps.201000544] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 11/30/2010] [Accepted: 12/29/2010] [Indexed: 11/07/2022]
Abstract
2-DE proved to be a key technology in protein science since the two orthogonal separation dimensions are capable of protein isoform separation. Recently, Agilent introduced the OFFGEL 3100 fractionator for in solution IEF (off-gel) of proteins with the help of a 12- or 24-well frame. With this instrument also conventional focusing in IPG strips after passive in-tray rehydration can be performed. In this study, two novel IEF applications using the OFFGEL electrophoresis were developed. First, a sample cup was built and a cup-loading method for the OFFGEL device was implemented. Applying proteins via cup resulted in higher reproducibility and less protein loss compared with conventional in-tray rehydration loading. Especially, the recovery of basic and high-molecular-mass proteins seems to be favored by cup loading. These effects are more pronounced with low microgram sample amounts. Second, a 48-well OFFGEL frame was developed, which doubles the resolution of the commercially available 24-well frame. It is capable of separating proteins with small pI differences and shows potential for isoform/PTM separation.
Collapse
Affiliation(s)
- Eva-Maria Keidel
- Max-Planck-Institute of Biochemistry, Protein Analysis Group, Martinsried, Germany.
| | | | | | | | | |
Collapse
|
16
|
Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G. Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. Mol Microbiol 2011; 80:1479-95. [PMID: 21535243 DOI: 10.1111/j.1365-2958.2011.07658.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The photosynthetic alphaproteobacterium Rhodobacter sphaeroides has to cope with photooxidative stress that is caused by the bacteriochlorophyll a-mediated formation of singlet oxygen ((1)O(2)). Exposure to (1)O(2) induces the alternative sigma factors RpoE and RpoH(II) which then promote transcription of photooxidative stress-related genes, including small RNAs (sRNAs). The ubiquitous RNA chaperone Hfq is well established to interact with and facilitate the base-pairing of sRNAs and target mRNAs to influence mRNA stability and/or translation. Here we report on the pleiotropic phenotype of a Δhfq mutant of R. sphaeroides, which is less pigmented, produces minicells and is more sensitive to (1)O(2). The higher (1)O(2) sensitivity of the Δhfq mutant is paralleled by a reduced RpoE activity and a disordered induction of RpoH(II)-dependent genes. We used co-immunoprecipitation of FLAG-tagged Hfq combined with RNA-seq to identify association of at least 25 sRNAs and of mRNAs encoding cell division proteins and ribosomal proteins with Hfq. Remarkably, > 70% of the Hfq-bound sRNAs are (1)O(2)-affected. Proteomics analysis of the Hfq-deficient strain revealed an impact of Hfq on amino acid transport and metabolic functions. Our data demonstrate for the first time an involvement of Hfq in regulation of photosynthesis genes and in the photooxidative stress response.
Collapse
Affiliation(s)
- Bork A Berghoff
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | | | | | | | | | | | | |
Collapse
|
17
|
Protze J, Müller F, Lauber K, Naß B, Mentele R, Lottspeich F, Kletzin A. An Extracellular Tetrathionate Hydrolase from the Thermoacidophilic Archaeon Acidianus Ambivalens with an Activity Optimum at pH 1. Front Microbiol 2011; 2:68. [PMID: 21747790 PMCID: PMC3128947 DOI: 10.3389/fmicb.2011.00068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 03/25/2011] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The thermoacidophilic and chemolithotrophic archaeon Acidianus ambivalens is routinely grown with sulfur and CO(2)-enriched air. We had described a membrane-bound, tetrathionate (TT) forming thiosulfate:quinone oxidoreductase. Here we describe the first TT hydrolase (TTH) from Archaea. RESULTS A. ambivalens cells grown aerobically with TT as sole sulfur source showed doubling times of 9 h and final cell densities of up to 8 × 10(8)/ml. TTH activity (≈0.28 U/mg protein) was found in cell-free extracts of TT-grown but not of sulfur-grown cells. Differential fractionation of freshly harvested cells involving a pH shock showed that about 92% of the TTH activity was located in the pseudo-periplasmic fraction associated with the surface layer, while 7.3% and 0.3% were present in the soluble and membrane fractions, respectively. The enzyme was enriched 54-fold from the cytoplasmic fraction and 2.1-fold from the pseudo-periplasmic fraction. The molecular mass of the single subunit was 54 kDa. The optimal activity was at or above 95°C at pH 1. Neither PQQ nor divalent cations had a significant effect on activity. The gene (tth1) was identified following N-terminal sequencing of the protein. Northern hybridization showed that tth1 was transcribed in TT-grown cells in contrast to a second paralogous tth2 gene. The deduced amino acid sequences showed similarity to the TTH from Acidithiobacillus and other proteins from the PQQ dehydrogenase superfamily. It displayed a β-propeller structure when being modeled, however, important residues from the PQQ-binding site were absent. CONCLUSION The soluble, extracellular, and acidophilic TTH identified in TT-grown A. ambivalens cells is essential for TT metabolism during growth but not for the downstream processing of the TQO reaction products in S°-grown cells. The liberation of TTH by pH shock from otherwise intact cells strongly supports the pseudo-periplasm hypothesis of the S-layer of Archaea.
Collapse
Affiliation(s)
- Jonas Protze
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Fabian Müller
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Karin Lauber
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Bastian Naß
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | | | | | - Arnulf Kletzin
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| |
Collapse
|
18
|
Obermeier B, Lovato L, Mentele R, Brück W, Forne I, Imhof A, Lottspeich F, Turk KW, Willis SN, Wekerle H, Hohlfeld R, Hafler DA, O'Connor KC, Dornmair K. Related B cell clones that populate the CSF and CNS of patients with multiple sclerosis produce CSF immunoglobulin. J Neuroimmunol 2011; 233:245-8. [PMID: 21353315 DOI: 10.1016/j.jneuroim.2011.01.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/19/2011] [Accepted: 01/26/2011] [Indexed: 02/01/2023]
Abstract
We investigated the overlap shared between the immunoglobulin (Ig) proteome of the cerebrospinal fluid (CSF) and the B cell Ig-transcriptome of CSF and the central nervous system (CNS) tissue of three patients with multiple sclerosis. We determined the IgG-proteomes of CSF by mass spectrometry, and compared them to the IgG-transcriptomes from CSF and brain lesions, which were analyzed by cDNA cloning. Characteristic peptides that were identified in the CSF-proteome could also be detected in the transcriptomes of both, brain lesions and CSF, providing evidence for a strong overlap of the IgG repertoires in brain lesions and in the CSF.
Collapse
Affiliation(s)
- Birgit Obermeier
- Institute of Clinical Neuroimmunology, Ludwig Maximilians University, 81377 Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Laimer M, Kocher T, Chiocchetti A, Trost A, Lottspeich F, Richter K, Hintner H, Bauer JW, Onder K. Proteomic profiling reveals a catalogue of new candidate proteins for human skin aging. Exp Dermatol 2011; 19:912-8. [PMID: 20849533 DOI: 10.1111/j.1600-0625.2010.01144.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Studies of skin aging are usually performed at the genomic level by investigating differentially regulated genes identified through subtractive hybridization or microarray analyses. In contrast, relatively few studies have investigated changes in protein expression of aged skin using proteomic profiling by two-dimensional (2-D) gel electrophoresis and mass spectrometry, although this approach at the protein level is suggested to reflect more accurately the aging phenotype. We undertook such a proteomic analysis of intrinsic human skin aging by quantifying proteins extracted and fluorescently labeled from sun-protected human foreskin samples pooled from 'young' and 'old' men. In addition, we analyzed these candidate gene products by 1-D and 2-D western blotting to obtain corroborative protein expression data, and by both real-time PCR (RT-PCR) and microarray analyses to confirm expression at the mRNA level. We discovered 30 putative proteins for skin aging, including previously unrecognized, post-translationally regulated candidates such as phosphatidyl-ethanolamine binding protein (PEBP) and carbonic anhydrase 1 (CA1).
Collapse
Affiliation(s)
- Martin Laimer
- Division of Molecular Dermatology, Department of Dermatology, Paracelsus Private Medical University Salzburg, Salzburg, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
Stable isotope labeling in combination with mass spectrometry has emerged as a powerful tool to identify and quantify thousands of proteins within complex protein mixtures. Isotope-coded protein label (ICPL) is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on stable isotope tagging at the free amino groups of intact proteins, it is applicable to any protein sample, including extracts from tissues or body fluids. After labeling of up to four different proteome states, the samples can be combined and the complexity reduced by any separation method currently employed in protein chemistry. After enzymatic cleavage of the protein fractions the ratios of peptides in the different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides that exhibit regulations in the different proteome states are further investigated for identification by tandem-mass spectrometry. The quantification of multiplexed ICPL experiments is greatly facilitated by the recently published ICPLQuant software, which was especially designed to cover the whole ICPL workflow. The method shows highly accurate and reproducible quantification of proteins, yields high sequence coverage, and is indispensable for the comprehensive detection of posttranslational modifications and protein isoforms.
Collapse
Affiliation(s)
- Friedrich Lottspeich
- Max Planck Institute of Biochemistry, Protein Analysis, D-82152, Martinsried, Germany.
| | | |
Collapse
|
21
|
Berghoff BA, Glaeser J, Nuss AM, Zobawa M, Lottspeich F, Klug G. Anoxygenic photosynthesis and photooxidative stress: a particular challenge for Roseobacter. Environ Microbiol 2010; 13:775-91. [DOI: 10.1111/j.1462-2920.2010.02381.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
22
|
|
23
|
Abstract
The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope-coded protein label (ICPL)-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time-consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS-identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker.
Collapse
Affiliation(s)
- Achim Brunner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| | | | | | | | | |
Collapse
|
24
|
Abstract
Despite worldwide efforts biomarker discovery by plasma proteomics was not successful so far. Several reasons for this failure are obvious. Mainly, proteome diversity is remarkable between different individuals and is caused by genetic, environmental and life style parameters. To recognize disease related proteins that could serve as potential biomarkers is only feasible by investigating a non realizable large number of patients. Furthermore, plasma proteomics comprises enormous technical hurdles for quantitative analysis. High reproducibility of blood sampling in clinical routine is hard to achieve. Quantitative proteome analysis has to struggle with the complexity of millions of protein species comprising typical plasma proteins, cellular leakage proteins and antibodies and concentration differences of more than 1011 between high and low abundant proteins. Therefore, no successful quantitative and comprehensive plasma proteome analysis is reported so far. A novel proteomics strategy is proposed for biomarker discovery in plasma. Instead of comparing the plasma proteome of different individuals it is recommended to analyze the proteomes of different time points of a single individual during the development of a disease. This strategy is realized by the use of plasma of the Bavarian Red Cross Blood Bank, were three million samples are stored under standardized conditions. To achieve reliable data the isotope coded protein labelling proteomics technology was used.
Collapse
|
25
|
Yang G, Li Q, Ren S, Lu X, Fang L, Zhou W, Zhang F, Xu F, Zhang Z, Zeng R, Lottspeich F, Chen Z. Proteomic, functional and motif-based analysis of C-terminal Src kinase-interacting proteins. Proteomics 2009; 9:4944-61. [PMID: 19743411 DOI: 10.1002/pmic.200800762] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
C-terminal Src kinase (Csk) that functions as an essential negative regulator of Src family tyrosine kinases (SFKs) interacts with tyrosine-phosphorylated molecules through its Src homology 2 (SH2) domain, allowing it targeting to the sites of SFKs and concomitantly enhancing its kinase activity. Identification of additional Csk-interacting proteins is expected to reveal potential signaling targets and previously undescribed functions of Csk. In this study, using a direct proteomic approach, we identified 151 novel potential Csk-binding partners, which are associated with a wide range of biological functions. Bioinformatics analysis showed that the majority of identified proteins contain one or several Csk-SH2 domain-binding motifs, indicating a potentially direct interaction with Csk. The interactions of Csk with four proteins (partitioning defective 3 (Par3), DDR1, SYK and protein kinase C iota) were confirmed using biochemical approaches and phosphotyrosine 1127 of Par3 C-terminus was proved to directly bind to Csk-SH2 domain, which was consistent with predictions from in silico analysis. Finally, immunofluorescence experiments revealed co-localization of Csk with Par3 in tight junction (TJ) in a tyrosine phosphorylation-dependent manner and overexpression of Csk, but not its SH2-domain mutant lacking binding to phosphotyrosine, promoted the TJ assembly in Madin-Darby canine kidney cells, implying the involvement of Csk-SH2 domain in regulating cellular TJs. In conclusion, the newly identified potential interacting partners of Csk provided new insights into its functional diversity in regulation of numerous cellular events, in addition to controlling the SFK activity.
Collapse
Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Barkhudaryan N, Zakaryan H, Sarukhanyan F, Gabrielyan A, Dosch D, Kellermann J, Lottspeich F. Hemorphins act as homeostatic agents in response to endotoxin-induced stress. Neurochem Res 2009; 35:925-33. [PMID: 19967445 DOI: 10.1007/s11064-009-0097-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
The effect of synthetic LVV-hemorphin-7 and hemorphin-7 on hypothalamo-pituitary-adrenocortical axis activity in response to endotoxin-induced stress was studied. The intraperitoneal (ip) endotoxin (lipopolysaccaride, LPS) (0.5 mg/kg) administration in combination with hemorphin (1 mg/kg) induce significant decrease in plasma corticosterone and modest decrease in plasma levels of tumor necrosis factor-alpha (TNFalpha) in compare with elevated levels of both corticosterone and TNFalpha in plasma of rats received LPS administration alone. Increased activity of calcineurin in both plasma and brain of rats received ip administration of LPS, was recovered under LPS + hemorphin treatment. In two independent proteome analysis, using 2-dimensional fluorescence difference gel electrophoresis and the isotope coded protein label technology, peptidyl-prolyl cis-trans-isomerase A (cyclophilin A) was identified as regulated by hemorphins protein in mouse brain. A therapeutic potential of hemorphins and mechanisms of their homeostatic action in response to endotoxin-induced stress are discussed.
Collapse
Affiliation(s)
- Nina Barkhudaryan
- H. Buniatian Institute of Biochemistry of National Academy of Sciences, 5/1 P. Sevag Str, Yerevan, 0014, Republic of Armenia.
| | | | | | | | | | | | | |
Collapse
|
27
|
Tebbe A, Schmidt A, Konstantinidis K, Falb M, Bisle B, Klein C, Aivaliotis M, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D. Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics 2009; 9:3843-55. [PMID: 19670246 DOI: 10.1002/pmic.200800944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Quantitative proteomics based on isotopic labeling has become the method of choice to accurately determine changes in protein abundance in highly complex mixtures. Isotope-coded protein labeling (ICPL), which is based on the nicotinoylation of proteins at lysine residues and free N-termini was used as a simple, reliable and fast method for the comparative analysis of three different cellular states of the halophilic archaeon Halobacterium salinarum through pairwise comparison. The labeled proteins were subjected to SDS-PAGE, in-gel digested and the proteolytic peptides were separated by LC and analyzed by MALDI-TOF/TOF MS. Automated quantitation was performed by comparing the MS peptide signals of (12)C and (13)C nicotinoylated isotopic peptide pairs. The transitions between (i) aerobic growth in complex versus synthetic medium and (ii) aerobic versus anaerobic/phototrophic growth, both in complex medium, provide a wide span in nutrient and energy supply for the cell and thus allowed optimal studies of proteome changes. In these two studies, 559 and 643 proteins, respectively, could be quantified allowing a detailed analysis of the adaptation of H. salinarum to changes of its living conditions. The subtle cellular response to a wide variation of nutrient and energy supply demonstrates a fine tuning of the cellular protein inventory.
Collapse
Affiliation(s)
- Andreas Tebbe
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: Current state and future fields of application in cellular proteomics. Cytometry A 2009; 75:816-32. [DOI: 10.1002/cyto.a.20779] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
29
|
Nägler DK, Kraus S, Feierler J, Mentele R, Lottspeich F, Jochum M, Faussner A. A cysteine-type carboxypeptidase, cathepsin X, generates peptide receptor agonists. Int Immunopharmacol 2009; 10:134-9. [PMID: 19800993 DOI: 10.1016/j.intimp.2009.09.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/17/2009] [Accepted: 09/24/2009] [Indexed: 01/06/2023]
Abstract
The kallikrein-kinin system and the renin-angiotensin system interact at different levels and are linked by various molecules such as angiotensin-converting enzyme which degrades bradykinin into inactive peptides. Here we report that a cysteine-type carboxypeptidase, cathepsin X, is able to modulate the kallikrein-kinin system through carboxyterminal processing of the small peptide hormones bradykinin and kallidin. Both peptides are thereby converted from bradykinin B(2) receptor ligands to bradykinin B(1) receptor specific ligands. Cathepsin X, which has previously been recognized as an inflammatory marker may therefore act as a type I kininase. In addition, we have identified cathepsin X as an alternative possible link between the kallikrein-kinin system and the renin-angiotensin system in that it not only cleaves kinins C-terminally, but also converts angiotensin I to angiotensin II.
Collapse
Affiliation(s)
- Dorit K Nägler
- Division of Clinical Chemistry and Clinical Biochemistry, Surgical Department, Ludwig-Maximilians-University, Munich, Germany.
| | | | | | | | | | | | | |
Collapse
|
30
|
Lichtenfels R, Dressler SP, Zobawa M, Recktenwald CV, Ackermann A, Atkins D, Kersten M, Hesse A, Puttkammer M, Lottspeich F, Seliger B. Systematic comparative protein expression profiling of clear cell renal cell carcinoma: a pilot study based on the separation of tissue specimens by two-dimensional gel electrophoresis. Mol Cell Proteomics 2009; 8:2827-42. [PMID: 19752005 DOI: 10.1074/mcp.m900168-mcp200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteome-based technologies represent powerful tools for the analysis of protein expression profiles, including the identification of potential cancer candidate biomarkers. Thus, here we provide a comprehensive protein expression map for clear cell renal cell carcinoma established by systematic comparative two-dimensional gel electrophoresis-based protein expression profiling of 16 paired tissue systems comprising clear cell renal cell carcinoma lesions and corresponding tumor-adjacent renal epithelium using overlapping narrow pH gradients. This approach led to the mapping of 348 distinct spots corresponding to 248 different protein identities. By implementing restriction criteria concerning their detection frequency and overall regulation mode, 28 up- and 56 down-regulated single target spots were considered as potential candidate biomarkers. Based on their gene ontology information, these differentially expressed proteins were classified into distinct functional groups and according to their cellular distribution. Moreover, three representative members of this group, namely calbindin, gelsolin, and heart fatty acid-binding protein, were selected, and their expression pattern was analyzed by immunohistochemistry using tissue microarrays. Thus, this pilot study provides a significant update of the current renal cell carcinoma map and defines a number of differentially expressed proteins, but both their potential as candidate biomarkers and clinical relevance has to be further explored in tissues and for body fluids like serum and urine.
Collapse
Affiliation(s)
- Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112 Halle/Saale, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Cook PF, Goto Y, Lottspeich F. Introduction to the special issue. Foreword. Biochim Biophys Acta 2009; 1794:1277-9. [PMID: 19695350 DOI: 10.1016/j.bbapap.2009.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Paul F Cook
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA.
| | | | | |
Collapse
|
32
|
Veith A, Klingl A, Zolghadr B, Lauber K, Mentele R, Lottspeich F, Rachel R, Albers SV, Kletzin A. Acidianus,SulfolobusandMetallosphaerasurface layers: structure, composition and gene expression. Mol Microbiol 2009; 73:58-72. [DOI: 10.1111/j.1365-2958.2009.06746.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Seliger B, Dressler SP, Wang E, Kellner R, Recktenwald CV, Lottspeich F, Marincola FM, Baumgärtner M, Atkins D, Lichtenfels R. Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma. Proteomics 2009; 9:1567-81. [PMID: 19235166 DOI: 10.1002/pmic.200700288] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Results obtained from expression profilings of renal cell carcinoma using different "ome"-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to up-regulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%), and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely three candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain, and ubiquitin carboxyl-terminal hydrolase L1, the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.
Collapse
Affiliation(s)
- Barbara Seliger
- Martin-Luther-University Halle-Wittenberg, Institute of Medical Immunology, Halle, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Pöll V, Denk U, Shen HD, Panzani RC, Dissertori O, Lackner P, Hemmer W, Mari A, Crameri R, Lottspeich F, Rid R, Richter K, Breitenbach M, Simon-Nobbe B. The vacuolar serine protease, a cross-reactive allergen from Cladosporium herbarum. Mol Immunol 2009; 46:1360-73. [DOI: 10.1016/j.molimm.2008.11.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 11/30/2022]
|
35
|
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med 2009; 47:724-44. [DOI: 10.1515/cclm.2009.167] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
36
|
Helm M, Schmid M, Hierl G, Terneus K, Tan L, Lottspeich F, Kieliszewski MJ, Gietl C. KDEL-tailed cysteine endopeptidases involved in programmed cell death, intercalation of new cells, and dismantling of extensin scaffolds. Am J Bot 2008; 95:1049-62. [PMID: 21632425 DOI: 10.3732/ajb.2007404] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
KDEL-tailed cysteine endopeptidases are a group of papain-type peptidases found in senescing tissue undergoing programmed cell death (PCD). Their genes have so far been cloned and analyzed in 12 angiosperms. They are synthesized as proenzymes with a C-terminal KDEL endoplasmatic reticulum retention signal, which is removed with the prosequence to activate enzyme activity. We previously identified three genes for KDEL-tailed cysteine endopeptidases (AtCEP1, AtCEP2, AtCEP3) in Arabidopsis thaliana. Transgenic plants of A. thaliana expressing β-glucuronidase (GUS) under the control of the promoters for the three genes were produced and analyzed histochemically. GUS activity was promoter- and tissue-specific GUS activity during seedling, flower, and root development, especially in tissues that collapse during final stages of PCD, and in the course of lateral root formation. KDEL-tailed cysteine endopeptidases are unique in being able to digest the extensins that form the basic scaffold for cell wall formation. The broad substrate specificity is due to the structure of the active site cleft of the KDEL-tailed cysteine endopeptidase that accepts a wide variety of amino acids, including proline and glycosylated hydroxyproline of the hydroxyproline rich glycoproteins of the cell wall.
Collapse
Affiliation(s)
- Michael Helm
- Technische Universität München, Lehrstuhl für Botanik, Biologikum-Weihenstephan, Am Hochanger 4, D-85350 Freising, Germany
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Samavati L, Lee I, Mathes I, Lottspeich F, Hüttemann M. Tumor necrosis factor alpha inhibits oxidative phosphorylation through tyrosine phosphorylation at subunit I of cytochrome c oxidase. J Biol Chem 2008; 283:21134-44. [PMID: 18534980 PMCID: PMC3258931 DOI: 10.1074/jbc.m801954200] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 05/06/2008] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial oxidative phosphorylation provides most cellular energy. As part of this process, cytochrome c oxidase (CcO) pumps protons across the inner mitochondrial membrane, contributing to the generation of the mitochondrial membrane potential, which is used by ATP synthase to produce ATP. During acute inflammation, as in sepsis, aerobic metabolism appears to malfunction and switches to glycolytic energy production. The pro-inflammatory cytokine tumor necrosis factor alpha (TNFalpha) has been shown to play a central role in inflammation. We hypothesized that TNFalpha-triggered cell signaling targets CcO, which is a central enzyme of the aerobic energy metabolism and can be regulated through phosphorylation. Using total bovine and murine hepatocyte homogenates TNFalpha treatment led to an approximately 60% reduction in CcO activity. In contrast, there was no direct effect of TNFalpha on CcO activity using isolated mitochondria and purified CcO, indicating that a TNFalpha-triggered intracellular signaling cascade mediates CcO inhibition. CcO isolated after TNFalpha treatment showed tyrosine phosphorylation on CcO catalytic subunit I and was approximately 50 and 70% inhibited at high cytochrome c concentrations in the presence of allosteric activator ADP and inhibitor ATP, respectively. CcO phosphorylation occurs on tyrosine 304 as demonstrated with a phosphoepitope-specific antibody. Furthermore, the mitochondrial membrane potential was decreased in H2.35 cells in response to TNFalpha. Concomitantly, cellular ATP was more than 35 and 64% reduced in murine hepatocytes and H2.35 cells. We postulate that an important contributor in TNFalpha-mediated pathologies, such as sepsis, is energy paucity, which parallels the poor tissue oxygen extraction and utilization found in such patients.
Collapse
Affiliation(s)
- Lobelia Samavati
- Department of Medicine,
Division of Pulmonary/Critical Care and Sleep Medicine, Wayne State University
School of Medicine, Detroit, Michigan 48201, the
Center for Molecular Medicine and
Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201,
and the Max Planck Institute of
Biochemistry, D-82152 Martinsried, Germany
| | - Icksoo Lee
- Department of Medicine,
Division of Pulmonary/Critical Care and Sleep Medicine, Wayne State University
School of Medicine, Detroit, Michigan 48201, the
Center for Molecular Medicine and
Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201,
and the Max Planck Institute of
Biochemistry, D-82152 Martinsried, Germany
| | - Isabella Mathes
- Department of Medicine,
Division of Pulmonary/Critical Care and Sleep Medicine, Wayne State University
School of Medicine, Detroit, Michigan 48201, the
Center for Molecular Medicine and
Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201,
and the Max Planck Institute of
Biochemistry, D-82152 Martinsried, Germany
| | - Friedrich Lottspeich
- Department of Medicine,
Division of Pulmonary/Critical Care and Sleep Medicine, Wayne State University
School of Medicine, Detroit, Michigan 48201, the
Center for Molecular Medicine and
Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201,
and the Max Planck Institute of
Biochemistry, D-82152 Martinsried, Germany
| | - Maik Hüttemann
- Department of Medicine,
Division of Pulmonary/Critical Care and Sleep Medicine, Wayne State University
School of Medicine, Detroit, Michigan 48201, the
Center for Molecular Medicine and
Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201,
and the Max Planck Institute of
Biochemistry, D-82152 Martinsried, Germany
| |
Collapse
|
38
|
Dunn MJ, Gil C, Kleinhammer C, Lottspeich F, Pennington S, Sanchez JC, Albar JP, Bini L, Corrales F, Corthals GL, Fountoulakis MM, Hoogland C, James P, Jensen ON, Jiménez C, Jorrín-Novo J, Kraus HJ, Meyer H, Noukakis D, Palagi PM, Penque D, Quinn A, Rabilloud T. EuPA achieves visibility - an activity report on the first three years. J Proteomics 2008; 71:11-8. [PMID: 18541470 DOI: 10.1016/j.jprot.2008.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 03/28/2008] [Accepted: 03/31/2008] [Indexed: 10/22/2022]
Abstract
Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteomics organizations in their efforts; ii) to co-ordinate and provide educational programs, and iii) to advance the networking of scientists through meetings, workshops and student exchange. Linked to the mission were objectives to emphasise the benefits and contributions of Proteomics to biological and industrial researchers, the general public and science policy makers in Europe. In addition, the EuPA set out to promote scientific exchange for all applications and technology development related to Proteomics, and coordinate joint activities of national Proteomics societies at the European level. To achieve these tasks an organisational structure was conceived whereby four Activity Committees (Conferences/Communications, Education, EuPA-HUPO-Interactions and Funding) were implemented and a General Council consisting of all member countries. The remarkable rise and progress the EuPA has achieved in this small time frame is reported here.
Collapse
Affiliation(s)
- M J Dunn
- UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Angermayr M, Hochleitner E, Lottspeich F, Bandlow W. Protein kinase CK2 activates the atypical Rio1p kinase and promotes its cell-cycle phase-dependent degradation in yeast. FEBS J 2007; 274:4654-67. [PMID: 17725716 DOI: 10.1111/j.1742-4658.2007.05993.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using co-immunoprecipitation combined with MS analysis, we identified the alpha' subunit of casein kinase 2 (CK2) as an interaction partner of the atypical Rio1 protein kinase in yeast. Co-purification of Rio1p with CK2 from Deltacka1 or Deltacka2 mutant extracts shows that Rio1p preferentially interacts with Cka2p in vitro. The C-terminal domain of Rio1p is essential and sufficient for this interaction. Six C-terminally located clustered serines were identified as the only CK2 sites present in Rio1p. Replacement of all six serine residues by aspartate, mimicking constitutive phosphorylation, stimulates Rio1p kinase activity about twofold in vitro compared with wild-type or the corresponding (S > A)(6) mutant proteins. Both mutant alleles (S > A)(6) or (S > D)(6) complement in vivo, however, growth of the RIO1 (S > A)(6) mutant is greatly retarded and shows a cell-cycle phenotype, whereas the behaviour of the RIO1 (S > D)(6) mutant is indistinguishable from wild-type. This suggests that phosphorylation by protein kinase CK2 leads to moderate activation of Rio1p in vivo and promotes cell proliferation. Physiological studies indicate that phosphorylation by CK2 renders the Rio1 protein kinase susceptible to proteolytic degradation at the G(1)/S transition in the cell-division cycle, whereas the non-phosphorylated version is resistant.
Collapse
Affiliation(s)
- Michaela Angermayr
- Department Biologie I, Bereich Genetik, Ludwig-Maximilians-Universität München, Germany.
| | | | | | | |
Collapse
|
40
|
Rassmann A, Henke A, Jarasch N, Lottspeich F, Saluz HP, Munder T. The human fatty acid synthase: a new therapeutic target for coxsackievirus B3-induced diseases? Antiviral Res 2007; 76:150-8. [PMID: 17662476 DOI: 10.1016/j.antiviral.2007.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 06/11/2007] [Accepted: 06/21/2007] [Indexed: 11/30/2022]
Abstract
Coxsackievirus is linked to a large variety of severe human and animal diseases such as myocarditis. The interplay between host factors and virus components is crucial for the fate of the infected cells. However, host proteins which may play a role in coxsackievirus-induced diseases are ill-defined. Two-dimensional gel electrophoresis of protein extracts obtained from coxsackievirus B3 (CVB3)-infected and uninfected HeLa or HepG2 cells combined with spot analysis revealed several proteins which are exclusively up-regulated in infected cells. One of these proteins was identified as the fatty acid synthase (FAS). By using cerulenin and C75, two known inhibitors of FAS we were able to significantly block CVB3 replication. FAS appears to be directly involved in CVB3-caused pathology and is therefore suitable as a therapeutic target in CVB3-induced diseases.
Collapse
Affiliation(s)
- Alexander Rassmann
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Department of Cell and Molecular Biology, Beutenbergstrasse 11a, D-07745 Jena, Germany
| | | | | | | | | | | |
Collapse
|
41
|
Helm M, Lück C, Prestele J, Hierl G, Huesgen PF, Fröhlich T, Arnold GJ, Adamska I, Görg A, Lottspeich F, Gietl C. Dual specificities of the glyoxysomal/peroxisomal processing protease Deg15 in higher plants. Proc Natl Acad Sci U S A 2007; 104:11501-6. [PMID: 17592111 PMCID: PMC2040927 DOI: 10.1073/pnas.0704733104] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glyoxysomes are a subclass of peroxisomes involved in lipid mobilization. Two distinct peroxisomal targeting signals (PTSs), the C-terminal PTS1 and the N-terminal PTS2, are defined. Processing of the PTS2 on protein import is conserved in higher eukaryotes. The cleavage site typically contains a Cys at P1 or P2. We purified the glyoxysomal processing protease (GPP) from the fat-storing cotyledons of watermelon (Citrullus vulgaris) by column chromatography, preparative native isoelectric focusing, and 2D PAGE. The GPP appears in two forms, a 72-kDa monomer and a 144-kDa dimer, which are in equilibrium with one another. The equilibrium is shifted on Ca(2+) removal toward the monomer and on Ca(2+) addition toward the dimer. The monomer is a general degrading protease and is activated by denatured proteins. The dimer constitutes the processing protease because the substrate specificity proven for the monomer (Phi-Arg/Lys downward arrow) is different from the processing substrate specificity (Cys-Xxx downward arrow/Xxx-Cys downward arrow) found with the mixture of monomer and dimer. The Arabidopsis genome analysis disclosed three proteases predicted to be in peroxisomes, a Deg-protease, a pitrilysin-like metallopeptidase, and a Lon-protease. Specific antibodies against the peroxisomal Deg-protease from Arabidopsis (Deg15) identify the watermelon GPP as a Deg15. A knockout mutation in the DEG15 gene of Arabidopsis (At1g28320) prevents processing of the glyoxysomal malate dehydrogenase precursor to the mature form. Thus, the GPP/Deg15 belongs to a group of trypsin-like serine proteases with Escherichia coli DegP as a prototype. Nevertheless, the GPP/Deg15 possesses specific characteristics and is therefore a new subgroup within the Deg proteases.
Collapse
Affiliation(s)
- Michael Helm
- Lehrstuhl für Botanik, Technische Universität München, Wissenschaftszentrum Weihenstephan, D-85350 Freising, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Glaeser J, Zobawa M, Lottspeich F, Klug G. Protein synthesis patterns reveal a complex regulatory response to singlet oxygen in Rhodobacter. J Proteome Res 2007; 6:2460-71. [PMID: 17536848 DOI: 10.1021/pr060624p] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Singlet oxygen (1O2) is a stress factor and signal in the facultative phototrophic bacterium Rhodobacter sphaeroides. In vivo protein labeling with L-[35S]-methionine and analysis by two-dimensional gel electrophoresis revealed that the synthesis of 61 proteins was changed in response to 1O2. After 1O2 treatment, protein synthesis patterns were distinct from those after H2O2 treatment but similar to those after high light exposure. This indicates regulatory mechanisms selective for different reactive oxygen species (ROS) and a response to light partly mediated by 1O2. Analysis of mutant strains support that the response to 1O2 is regulated mainly by rpoE (sigma E), but also a modulation of the sigma E dependent response by other factors and the existence of sigma E independent responses. The involvement of the RNA chaperon Hfq in the 1O2 response implies a role of small regulatory RNAs.
Collapse
Affiliation(s)
- Jens Glaeser
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
| | | | | | | |
Collapse
|
43
|
Li X, Kaloyanova D, van Eijk M, Eerland R, van der Goot G, Oorschot V, Klumperman J, Lottspeich F, Starkuviene V, Wieland FT, Helms JB. Involvement of a Golgi-resident GPI-anchored protein in maintenance of the Golgi structure. Mol Biol Cell 2007; 18:1261-71. [PMID: 17251550 PMCID: PMC1838991 DOI: 10.1091/mbc.e06-03-0236] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Revised: 12/22/2006] [Accepted: 01/12/2007] [Indexed: 01/08/2023] Open
Abstract
The Golgi apparatus consists of a series of flattened cisternal membranes that are aligned in parallel to form stacks. Cytosolic-oriented Golgi-associated proteins have been identified that may coordinate or maintain the Golgi architecture. Here, we describe a novel GPI-anchored protein, Golgi-resident GPI-anchored protein (GREG) that has a brefeldin A-sensitive Golgi localization. GREG resides in the Golgi lumen as a cis-oriented homodimer, due to strong interactions between coiled-coil regions in the C termini. Dimerization of GREG as well as its Golgi localization depends on a unique tandem repeat sequence within the coiled-coil region. RNA-mediated interference of GREG expression or expression of GREG mutants reveals an essential role for GREG in maintenance of the Golgi integrity. Under these conditions, secretion of the vesicular stomatitis virus glycoprotein protein as a marker for protein transport along the secretory pathway is inhibited, suggesting a loss of Golgi function as well. These results imply the involvement of a luminal protein in Golgi structure and function.
Collapse
Affiliation(s)
- Xueyi Li
- *Biochemie-Zentrum Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Dora Kaloyanova
- Department of Biochemistry and Cell Biology and Institute of Biomembranes, Utrecht University, 3508 TD Utrecht, The Netherlands
| | - Martin van Eijk
- Department of Biochemistry and Cell Biology and Institute of Biomembranes, Utrecht University, 3508 TD Utrecht, The Netherlands
| | - Ruud Eerland
- Department of Biochemistry and Cell Biology and Institute of Biomembranes, Utrecht University, 3508 TD Utrecht, The Netherlands
| | - Gisou van der Goot
- Institut des Maladies Infectieuses, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Viola Oorschot
- Department of Cell Biology, University Medical Center and Institute for Biomembranes, 3584 CX Utrecht, The Netherlands
| | - Judith Klumperman
- Department of Cell Biology, University Medical Center and Institute for Biomembranes, 3584 CX Utrecht, The Netherlands
| | | | - Vytaute Starkuviene
- Cell Biology and Biophysics Programme, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Felix T. Wieland
- *Biochemie-Zentrum Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - J. Bernd Helms
- Department of Biochemistry and Cell Biology and Institute of Biomembranes, Utrecht University, 3508 TD Utrecht, The Netherlands
- *Biochemie-Zentrum Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| |
Collapse
|
44
|
Bresgen N, Ohlenschläger I, Fiedler B, Wacht N, Zach S, Dunkelmann B, Arosio P, Kuffner E, Lottspeich F, Eckl PM. Ferritin-a mediator of apoptosis? J Cell Physiol 2007; 212:157-64. [PMID: 17348034 DOI: 10.1002/jcp.21009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previously we have demonstrated an apoptosis inducing activity for a rat hepatocyte conditioned medium (CM) presumably mediated by acidic isoferritins. Here, we present support for this assumption since isoferritins purified from different rat hepatocyte CM significantly enhanced the frequency of apoptotic cells in primary rat hepatocytes, an effect completely inhibited by a neutralizing anti-H-ferritin antibody. The apoptosis induction appears to be related to a 43 kDa ferritin subunit contained in the isoferritins released from primary hepatocytes, presumably representing a ferritin heavy/light chain heterodimer. In addition, these isoferritins immunologically crossreact with antibodies raised against placental isoferritin p43-PLF (which also contains a 43 kDa ferritin subunit) and melanoma-derived H-chain ferritin, representing ferritin isoforms which reveal immunomodulatory properties. Furthermore, p53 and FasL are upregulated upon isoferritin treatment in a time dependent mode, and apoptosis induction can be suppressed by neutralizing anti-FasL antibodies. Proapoptotic Bid is upregulated too and translocated into mitochondria in primary hepatocytes exposed to the isoferritins purified from the CM. Finally, epidermal growth factor (EGF) and dexamethasone (DEX), which counteract proapoptotic mitochondrial signalling, almost completely abolished the proapoptotic effect of the hepatocyte derived isoferritins. In conclusion, our findings demonstrate that acidic isoferritins with homology to immunomodulatory ferritin isoforms (p43-PLF, melanoma-derived-H-chain ferritin) are released from hepatocytes in vitro, and are able to stimulate upregulation of p53 and mediate apoptosis involving Fas (CD95) signalling as well as addressing the intrinsic mitochondrial proapoptotic pathway.
Collapse
Affiliation(s)
- Nikolaus Bresgen
- Department of Cell Biology, University of Salzburg, Salzburg, Austria.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Schrader R, Young C, Kozian D, Hoffmann R, Lottspeich F. Temperature-sensitive eIF5A mutant accumulates transcripts targeted to the nonsense-mediated decay pathway. J Biol Chem 2006; 281:35336-46. [PMID: 16987817 DOI: 10.1074/jbc.m601460200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The highly conserved protein eIF5A found in Archaea and all eukaryotes uniquely contains the posttranslationally formed amino acid hypusine. Despite being essential the functions of this protein and its modification remain unclear. To gain more insight into these functions temperature-sensitive mutants of the human EIF5A1 were characterized in the yeast Saccharomyces cerevisiae. Expression of the point mutated form V81G in a DeltaeIF5A strain of yeast led to a strongly temperature-sensitive phenotype and to a significantly reduced protein level at restrictive temperature. The mutant showed accumulation of a subset of mRNAs that was also observed in nonsense-mediated decay (NMD)-deficient yeast strains. After short incubation at restrictive temperature the mutant exhibited increased half-lives of the intron containing CYH2 pre-mRNA and mature transcripts of NMD-dependent genes. Reduced telomere silencing and shortening was detected in the V81G mutant further supporting similarities to NMD-deficient strains. Our data suggest that eIF5A mediates important cellular processes like cell viability and senescence through its effects on the stability of certain mRNAs.
Collapse
Affiliation(s)
- Rainer Schrader
- Department for Protein Analytics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | | | | | | | | |
Collapse
|
46
|
Tabbert A, Kappes F, Knippers R, Kellermann J, Lottspeich F, Ferrando-May E. Hypophosphorylation of the architectural chromatin protein DEK in death-receptor-induced apoptosis revealed by the isotope coded protein label proteomic platform. Proteomics 2006; 6:5758-72. [PMID: 17001602 DOI: 10.1002/pmic.200600197] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
During apoptosis nuclear morphology changes dramatically due to alterations of chromatin architecture and cleavage of structural nuclear proteins. To characterize early events in apoptotic nuclear dismantling we have performed a proteomic study of apoptotic nuclei. To this end we have combined a cell-free apoptosis system with a proteomic platform based on the differential isotopic labeling of primary amines with N-nicotinoyloxy-succinimide. We exploited the ability of this system to produce nuclei arrested at different stages of apoptosis to analyze proteome alterations which occur prior to or at a low level of caspase activation. We show that the majority of proteins affected at the onset of apoptosis are involved in chromatin architecture and RNA metabolism. Among them is DEK, an architectural chromatin protein which is linked to autoimmune disorders. The proteomic analysis points to the occurrence of multiple PTMs in early apoptotic nuclei. This is confirmed by showing that the level of phosphorylation of DEK is decreased following apoptosis induction. These results suggest the unexpected existence of an early crosstalk between cytoplasm and nucleus during apoptosis. They further establish a previously unrecognized link between DEK and cell death, which will prove useful in the elucidation of the physiological function of this protein.
Collapse
Affiliation(s)
- Anja Tabbert
- University of Konstanz, Molecular Toxicology Group, Konstanz, Germany
| | | | | | | | | | | |
Collapse
|
47
|
Wang Y, Du D, Fang L, Yang G, Zhang C, Zeng R, Ullrich A, Lottspeich F, Chen Z. Tyrosine phosphorylated Par3 regulates epithelial tight junction assembly promoted by EGFR signaling. EMBO J 2006; 25:5058-70. [PMID: 17053785 PMCID: PMC1630420 DOI: 10.1038/sj.emboj.7601384] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 09/12/2006] [Indexed: 11/08/2022] Open
Abstract
The conserved polarity complex, comprising the partitioning-defective (Par) proteins Par3 and Par6, and the atypical protein kinase C, functions in various cell-polarization events and asymmetric cell divisions. However, little is known about whether and how external stimuli-induced signals may regulate Par3 function in epithelial cell polarity. Here, we found that Par3 was tyrosine phosphorylated through phosphoproteomic profiling of pervanadate-induced phosphotyrosine proteins. We also demonstrated that the tyrosine phosphorylation event induced by multiple growth factors including epidermal growth factor (EGF) was dependent on activation of Src family kinase (SFK) members c-Src and c-Yes. The tyrosine residue 1127 (Y1127) of Par3 was identified as the major EGF-induced phosphorylation site. Moreover, we found that Y1127 phosphorylation reduced the association of Par3 with LIM kinase 2 (LIMK2), thus enabling LIMK2 to regulate cofilin phosphorylation dynamics. Substitution of Y1127 for phenylalanine impaired the EGF-induced Par3 and LIMK2 dissociation and delayed epithelial tight junction (TJ) assembly considerably. Collectively, these data suggest a novel, phosphotyrosine-dependent fine-tuning mechanism of Par3 in epithelial TJ assembly controlled by the EGF receptor-SFK signaling pathway.
Collapse
Affiliation(s)
- Yiguo Wang
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Dan Du
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Longhou Fang
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Guang Yang
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Chenyi Zhang
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rong Zeng
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Axel Ullrich
- Department of Molecular Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | | | - Zhengjun Chen
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- SHARF Laboratory, Shanghai, China
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China. Tel.: 86 21 54921081; Fax: 86 21 54921081; E-mail:
| |
Collapse
|
48
|
Rassmann A, Henke A, Zobawa M, Carlsohn M, Saluz HP, Grabley S, Lottspeich F, Munder T. Proteome alterations in human host cells infected with coxsackievirus B3. J Gen Virol 2006; 87:2631-2638. [PMID: 16894202 DOI: 10.1099/vir.0.81819-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Coxsackievirus B3 (CVB3) is a common factor in human myocarditis. The interplay between host factors and virus components is crucial for the fate of the infected cells. Despite that, host protein responses, which characterize CVB3-induced diseases, have not yet been determined in detail. To investigate the nature of modified protein patterns in infected human cells compared with uninfected cells, two-dimensional gel electrophoresis in combination with matrix-assisted laser desorption/ionization-mass spectrometry were used. The regulated proteins, e.g. nucleophosmin (nucleolar protein B23), lamin, the RNA-binding protein UNR and the p38 mitogen-activated protein kinase, were sorted according to their functional groups and interpreted in the context of the myocarditis process.
Collapse
Affiliation(s)
- Alexander Rassmann
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Andreas Henke
- Institute of Virology and Antiviral Therapy, Medical Center, Friedrich Schiller University, Hans-Knoell-Strasse 2, D-07745 Jena, Germany
| | - Monica Zobawa
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Marc Carlsohn
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Hans-Peter Saluz
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Susanne Grabley
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Friedrich Lottspeich
- Institute of Virology and Antiviral Therapy, Medical Center, Friedrich Schiller University, Hans-Knoell-Strasse 2, D-07745 Jena, Germany
| | - Thomas Munder
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstrasse 11a, D-07745 Jena, Germany
| |
Collapse
|
49
|
Debela M, Magdolen V, Schechter N, Valachova M, Lottspeich F, Craik CS, Choe Y, Bode W, Goettig P. Specificity Profiling of Seven Human Tissue Kallikreins Reveals Individual Subsite Preferences. J Biol Chem 2006; 281:25678-88. [PMID: 16740631 DOI: 10.1074/jbc.m602372200] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human tissue kallikreins (hKs) form a family of 15 closely related (chymo)trypsin-like serine proteinases. These tissue kallikreins are expressed in a wide range of tissues including the central nervous system, the salivary gland, and endocrine-regulated tissues, such as prostate, breast, or testis, and may have diverse physiological functions. For several tissue kallikreins, a clear correlation has been established between expression and different types of cancer. For example, the prostate-specific antigen (PSA or hK3) serves as tumor marker and is used to monitor therapy response. Using a novel strategy, we have cloned, expressed in Escherichia coli or in insect cells, refolded, activated, and purified the seven human tissue kallikreins hK3/PSA, hK4, hK5, hK6, hK7, hK10, and hK11. Moreover, we have determined their extended substrate specificity for the nonprime side using a positional scanning combinatorial library of tetrapeptide substrates. hK3/PSA and hK7 exhibited a chymotrypsin-like specificity preferring large hydrophobic or polar residues at the P1 position. In contrast, hK4, hK5, and less stringent hK6 displayed a trypsin-like specificity with strong preference for P1-Arg, whereas hK10 and hK11 showed an ambivalent specificity, accepting both basic and large aliphatic P1 residues. The extended substrate specificity profiles are in good agreement with known substrate cleavage sites but also in accord with experimentally solved (hK4, hK6, and hK7) or modeled structures. The specificity profiles may lead to a better understanding of human tissue kallikrein functions and assist in identifying their physiological protein substrates as well as in designing more selective inhibitors.
Collapse
Affiliation(s)
- Mekdes Debela
- Max-Planck-Institut für Biochemie, Proteinase Research Group, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D. Quantitative Profiling of the Membrane Proteome in a Halophilic Archaeon. Mol Cell Proteomics 2006; 5:1543-58. [PMID: 16804162 DOI: 10.1074/mcp.m600106-mcp200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present a large scale quantitation study of the membrane proteome from Halobacterium salinarum. To overcome problems generally encountered with membrane proteins, we established a membrane preparation protocol that allows the application of most proteomic techniques originally developed for soluble proteins. Proteins were quantified using two complementary approaches. For gel-based quantitation, DIGE labeling was combined with two-dimensional gel electrophoresis on an improved 16-benzyldimethyl-n-hexadecylammonium chloride/SDS system. MS-based quantitation was carried out by combining gel-free separation with the recently developed isotope-coded protein labeling technique. Good correlations between these two independent quantitation strategies were obtained. From computational analysis we conclude that labeling of free amino groups by isotope-coded protein labeling (Lys and free N termini) is better suited for membrane proteins than Cys-based labeling strategies but that quantitation of integral membrane proteins remains cumbersome compared with soluble proteins. Nevertheless we could quantify 155 membrane proteins; 101 of these had transmembrane domains. We compared two growth states that strongly affect the energy supply of the cells: aerobic versus anaerobic/phototrophic conditions. The photosynthetic protein bacteriorhodopsin is the most highly regulated protein. As expected, several other membrane proteins involved in aerobic or anaerobic energy metabolism were found to be regulated, but in total, however, the number of regulated proteins is rather small.
Collapse
Affiliation(s)
- Birgit Bisle
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|