1
|
Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI, Ralser M. dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat Commun 2022; 13:3944. [PMID: 35803928 PMCID: PMC9270362 DOI: 10.1038/s41467-022-31492-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/20/2022] [Indexed: 11/28/2022] Open
Abstract
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm and generation of optimized spectral libraries, as well as take advantage of neural network-based processing of dia-PASEF data. Our computational platform boosts proteomic depth by up to 83% compared to previous work, and is specifically beneficial for fast proteomic experiments and those with low sample amounts. It quantifies over 5300 proteins in single injections recorded at 200 samples per day throughput using Evosep One chromatography system on a timsTOF Pro mass spectrometer and almost 9000 proteins in single injections recorded with a 93-min nanoflow gradient on timsTOF Pro 2, from 200 ng of HeLa peptides. A user-friendly implementation is provided through the incorporation of the algorithms in the DIA-NN software and by the FragPipe workflow for spectral library generation.
Collapse
Affiliation(s)
- Vadim Demichev
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry and Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Agathe Niewienda
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Daniela Ludwig
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Kathryn S Lilley
- Department of Biochemistry and Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- Core Facility High-Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Markus Ralser
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| |
Collapse
|
2
|
Rademacher S, Detering NT, Schüning T, Lindner R, Santonicola P, Wefel IM, Dehus J, Walter LM, Brinkmann H, Niewienda A, Janek K, Varela MA, Bowerman M, Di Schiavi E, Claus P. A Single Amino Acid Residue Regulates PTEN-Binding and Stability of the Spinal Muscular Atrophy Protein SMN. Cells 2020; 9:cells9112405. [PMID: 33153033 PMCID: PMC7692393 DOI: 10.3390/cells9112405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disease caused by decreased levels of the survival of motoneuron (SMN) protein. Post-translational mechanisms for regulation of its stability are still elusive. Thus, we aimed to identify regulatory phosphorylation sites that modulate function and stability. Our results show that SMN residues S290 and S292 are phosphorylated, of which SMN pS290 has a detrimental effect on protein stability and nuclear localization. Furthermore, we propose that phosphatase and tensin homolog (PTEN), a novel phosphatase for SMN, counteracts this effect. In light of recent advancements in SMA therapies, a significant need for additional approaches has become apparent. Our study demonstrates S290 as a novel molecular target site to increase the stability of SMN. Characterization of relevant kinases and phosphatases provides not only a new understanding of SMN function, but also constitutes a novel strategy for combinatorial therapeutic approaches to increase the level of SMN in SMA.
Collapse
Affiliation(s)
- Sebastian Rademacher
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Nora T. Detering
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Tobias Schüning
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Robert Lindner
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Pamela Santonicola
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Inga-Maria Wefel
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Janina Dehus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Lisa M. Walter
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Hella Brinkmann
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Agathe Niewienda
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Katharina Janek
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Miguel A. Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- Department of Paediatrics, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Melissa Bowerman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Elia Di Schiavi
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Peter Claus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
- Correspondence:
| |
Collapse
|
3
|
Kuckelkorn U, Stübler S, Textoris-Taube K, Kilian C, Niewienda A, Henklein P, Janek K, Stumpf MPH, Mishto M, Liepe J. Proteolytic dynamics of human 20S thymoproteasome. J Biol Chem 2019; 294:7740-7754. [PMID: 30914481 DOI: 10.1074/jbc.ra118.007347] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/26/2019] [Indexed: 01/22/2023] Open
Abstract
An efficient immunosurveillance of CD8+ T cells in the periphery depends on positive/negative selection of thymocytes and thus on the dynamics of antigen degradation and epitope production by thymoproteasome and immunoproteasome in the thymus. Although studies in mouse systems have shown how thymoproteasome activity differs from that of immunoproteasome and strongly impacts the T cell repertoire, the proteolytic dynamics and the regulation of human thymoproteasome are unknown. By combining biochemical and computational modeling approaches, we show here that human 20S thymoproteasome and immunoproteasome differ not only in the proteolytic activity of the catalytic sites but also in the peptide transport. These differences impinge upon the quantity of peptide products rather than where the substrates are cleaved. The comparison of the two human 20S proteasome isoforms depicts different processing of antigens that are associated to tumors and autoimmune diseases.
Collapse
Affiliation(s)
- Ulrike Kuckelkorn
- From the Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institut für Biochemie, Germany, 10117 Berlin, Germany
| | - Sabine Stübler
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.,Mathematical Modelling and Systems Biology, Institute of Mathematics, University of Potsdam, 14469 Potsdam, Germany
| | - Kathrin Textoris-Taube
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie, Germany, 10117 Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Shared Facility for Mass Spectrometry, 10117 Berlin, Germany
| | - Christiane Kilian
- From the Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institut für Biochemie, Germany, 10117 Berlin, Germany
| | - Agathe Niewienda
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie, Germany, 10117 Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Shared Facility for Mass Spectrometry, 10117 Berlin, Germany
| | - Petra Henklein
- From the Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institut für Biochemie, Germany, 10117 Berlin, Germany
| | - Katharina Janek
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie, Germany, 10117 Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Shared Facility for Mass Spectrometry, 10117 Berlin, Germany
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.,Melbourne Integrative Genomics, Schools of BioSciences and of Maths & Stats, University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Michele Mishto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie, Germany, 10117 Berlin, Germany, .,Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, School of Immunology and Microbial Science, King's College London, London SE1 1UL, United Kingdom
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom, .,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and
| |
Collapse
|
4
|
Gehring T, Heydeck D, Niewienda A, Janek K, Kuhn H. Do lipoxygenases occur in viruses?: Expression and characterization of a viral lipoxygenase-like protein did not provide evidence for the existence of functional viral lipoxygenases. Prostaglandins Leukot Essent Fatty Acids 2018; 138:14-23. [PMID: 30392576 DOI: 10.1016/j.plefa.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/24/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023]
Abstract
Lipoxygenases are lipid peroxidizing enzymes, which frequently occur in higher plants and animals. In bacteria, these enzymes are rare and have been introduced via horizontal gene transfer. Since viruses function as horizontal gene transfer vectors and since lipoxygenases may be helpful for releasing assembled virus particles from host cells we explored whether these enzymes may actually occur in viruses. For this purpose we developed a four-step in silico screening strategy and searching the publically available viral genomes for lipoxygenase-like sequences we detected a single functional gene in the genome of a mimivirus infecting Acantamoeba polyphaga. The primary structure of this protein involved two putative metal ligand clusters but the recombinant enzyme did neither contain iron nor manganese. Most importantly, it did not exhibit lipoxygenase activity. These data suggests that this viral lipoxygenase-like sequence does not encode a functional lipoxygenase and that these enzymes do not occur in viruses.
Collapse
Affiliation(s)
- Tatjana Gehring
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Dagmar Heydeck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany.
| |
Collapse
|
5
|
Midha A, Janek K, Niewienda A, Henklein P, Guenther S, Serra DO, Schlosser J, Hengge R, Hartmann S. Corrigendum: The Intestinal Roundworm Ascaris suum Releases Antimicrobial Factors Which Interfere With Bacterial Growth and Biofilm Formation. Front Cell Infect Microbiol 2018; 8:367. [PMID: 30364807 PMCID: PMC6198275 DOI: 10.3389/fcimb.2018.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fcimb.2018.00271.].
Collapse
Affiliation(s)
- Ankur Midha
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Berlin, Germany
| | - Petra Henklein
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Berlin, Germany
| | - Sebastian Guenther
- Department of Veterinary Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany.,Department of Pharmaceutical Biology, Institute of Pharmacy, Ernst-Moritz-Arndt-Universität Greifswald, Greifswald, Germany
| | - Diego O Serra
- Institute of Biology/Microbiology, Humboldt-Universität-zu-Berlin, Berlin, Germany
| | - Josephine Schlosser
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Regine Hengge
- Institute of Biology/Microbiology, Humboldt-Universität-zu-Berlin, Berlin, Germany
| | - Susanne Hartmann
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
6
|
Midha A, Janek K, Niewienda A, Henklein P, Guenther S, Serra DO, Schlosser J, Hengge R, Hartmann S. The Intestinal Roundworm Ascaris suum Releases Antimicrobial Factors Which Interfere With Bacterial Growth and Biofilm Formation. Front Cell Infect Microbiol 2018; 8:271. [PMID: 30131945 PMCID: PMC6090379 DOI: 10.3389/fcimb.2018.00271] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 05/02/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022] Open
Abstract
Ascariasis is a widespread soil-transmitted helminth infection caused by the intestinal roundworm Ascaris lumbricoides in humans, and the closely related Ascaris suum in pigs. Progress has been made in understanding interactions between helminths and host immune cells, but less is known concerning the interactions of parasitic nematodes and the host microbiota. As the host microbiota represents the direct environment for intestinal helminths and thus a considerable challenge, we studied nematode products, including excretory-secretory products (ESP) and body fluid (BF), of A. suum to determine their antimicrobial activities. Antimicrobial activities against gram-positive and gram-negative bacterial strains were assessed by the radial diffusion assay, while effects on biofilm formation were assessed using the crystal violet static biofilm and macrocolony assays. In addition, bacterial neutralizing activity was studied by an agglutination assay. ESP from different A. suum life stages (in vitro-hatched L3, lung-stage L3, L4, and adult) as well as BF from adult males were analyzed by mass spectrometry. Several proteins and peptides with known and predicted roles in nematode immune defense were detected in ESP and BF samples, including members of A. suum antibacterial factors (ASABF) and cecropin antimicrobial peptide families, glycosyl hydrolase enzymes such as lysozyme, as well as c-type lectin domain-containing proteins. Native, unconcentrated nematode products from intestine-dwelling L4-stage larvae and adults displayed broad-spectrum antibacterial activity. Additionally, adult A. suum ESP interfered with biofilm formation by Escherichia coli, and caused bacterial agglutination. These results indicate that A. suum uses a variety of factors with broad-spectrum antibacterial activity to affirm itself within its microbe-rich environment in the gut.
Collapse
Affiliation(s)
- Ankur Midha
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Berlin, Germany
| | - Petra Henklein
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Berlin, Germany
| | - Sebastian Guenther
- Department of Veterinary Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany.,Department of Pharmaceutical Biology, Institute of Pharmacy, Ernst-Moritz-Arndt-Universität Greifswald, Greifswald, Germany
| | - Diego O Serra
- Institute of Biology/Microbiology, Humboldt-Universität-zu-Berlin, Berlin, Germany
| | - Josephine Schlosser
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Regine Hengge
- Institute of Biology/Microbiology, Humboldt-Universität-zu-Berlin, Berlin, Germany
| | - Susanne Hartmann
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
7
|
Sofi S, Stehling S, Niewienda A, Janek K, Kuhn H, Ufer C. Functional characterization of isolated RNA-binding domains of the GRSF1 protein. Biochim Biophys Acta Gen Subj 2017; 1862:946-957. [PMID: 29288125 DOI: 10.1016/j.bbagen.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 11/26/2022]
Abstract
The Guanine-rich RNA sequence binding factor 1 (GRSF1) is a member of the heterogeneous nuclear ribonucleoprotein F/H family and has been implicated in RNA processing, RNA transport and translational regulation. Amino acid alignments and homology modeling suggested the existence of three distinct RNA-binding domains and two auxiliary domains. Unfortunately, little is known about the molecular details of GRSF1/RNA interactions. To explore the RNA-binding mechanisms we first expressed full-length human GRSF1 and several truncation mutants, which include the three separated qRRM domains in E. coli, purified the recombinant proteins and quantified their RNA-binding affinity by RNA electrophoretic mobility shift assays. The expression levels varied between 1 and 10mg purified protein per L bacterial liquid culture and for full-length human GRSF1 a binding constant (KD-value) of 0.5μM was determined. In addition, our mechanistic experiments with different truncation mutants allowed the following conclusions: i) Deletion of either of the three RNA-binding domains impaired the RNA-binding affinity suggesting that the simultaneous presence of the three domains is essential for high-affinity RNA-binding. ii) Deletion of the Ala-rich auxiliary domain did hardly affect RNA-binding. Thus, this structural subunit may not be involved in RNA interaction. iii) Deletion of the acidic auxiliary domain improved the RNA-binding suggesting a regulatory role for this structural motif. iv) The isolated RNA-binding domains did not exhibit sizeable RNA-binding affinities. Taken together these data suggest that a cooperative interaction of the three qRRMs is required for high affinity RNA-binding.
Collapse
Affiliation(s)
- Sajad Sofi
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Sabine Stehling
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Christoph Ufer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany.
| |
Collapse
|
8
|
Janek K, Niewienda A, Wöstemeyer J, Voigt J. The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors. Food Chem 2016; 211:320-8. [DOI: 10.1016/j.foodchem.2016.05.033] [Citation(s) in RCA: 21] [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] [Received: 01/23/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 11/26/2022]
|
9
|
Janek K, Niewienda A, Wöstemeyer J, Voigt J. Dataset of cocoa aspartic protease cleavage sites. Data Brief 2016; 8:700-8. [PMID: 27508221 PMCID: PMC4950170 DOI: 10.1016/j.dib.2016.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 05/30/2016] [Accepted: 06/14/2016] [Indexed: 11/17/2022] Open
Abstract
The data provide information in support of the research article, "The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors" (Janek et al., 2016) [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS) and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans.
Collapse
Affiliation(s)
- Katharina Janek
- Charité – University Medicine Berlin, Institute of Biochemistry, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité – University Medicine Berlin, Institute of Biochemistry, D-10117 Berlin, Germany
| | - Johannes Wöstemeyer
- Friedrich-Schiller-University Jena, Chair of General Microbiology and Microbial Genetics, D-07743 Jena, Germany
| | - Jürgen Voigt
- Friedrich-Schiller-University Jena, Chair of General Microbiology and Microbial Genetics, D-07743 Jena, Germany
- Corresponding author.
| |
Collapse
|
10
|
Voigt J, Janek K, Textoris-Taube K, Niewienda A, Wöstemeyer J. Partial purification and characterisation of the peptide precursors of the cocoa-specific aroma components. Food Chem 2016; 192:706-13. [DOI: 10.1016/j.foodchem.2015.07.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/25/2015] [Accepted: 07/16/2015] [Indexed: 10/23/2022]
|
11
|
Ebner F, Hepworth MR, Rausch S, Janek K, Niewienda A, Kühl A, Henklein P, Lucius R, Hamelmann E, Hartmann S. Therapeutic potential of larval excretory/secretory proteins of the pig whipworm Trichuris suis in allergic disease. Allergy 2014; 69:1489-97. [PMID: 25069662 DOI: 10.1111/all.12496] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND Gastrointestinal nematodes are currently being evaluated as a novel therapeutic in the treatment of chronic human inflammatory disorders, due to their unique ability to induce immunoregulatory pathways in their hosts. In particular, administration of ova from the pig whipworm Trichuris suis (T. suis; TSO) has been proposed for the treatment of allergic, inflammatory and autoimmune disorders. Despite these advances, the biological pathways through which TSO therapy modulates the host immune system in the context of human disease remain undefined. METHODS We characterized the dominant proteins present in the excretory/secretory (E/S) products of first-stage (L1) T. suis larvae (Ts E/S) using LC-MS/MS analysis and examined the immunosuppressive properties of whole larval Ts E/S in vitro and in a murine model of allergic airway disease. RESULTS Administration of larval Ts E/S proteins in vivo during the allergen sensitization phase was sufficient to suppress airway hyperreactivity, bronchiolar inflammatory infiltrate and allergen-specific IgE production. Three proteins in larval Ts E/S were unambiguously identified. The immunomodulatory function of larval Ts E/S was found to be partially dependent on the immunoregulatory cytokine IL-10. CONCLUSIONS Taken together, these data demonstrate that the released proteins of larval T. suis have significant immunomodulatory capacities and efficiently dampen allergic airway hyperreactivity. Thus, the therapeutic potential of defined larval E/S proteins should be exploited for the treatment of human allergic disorders.
Collapse
Affiliation(s)
- F. Ebner
- Institute of Immunology; Freie Universität Berlin; Berlin Germany
| | - M. R. Hepworth
- Institute of Immunology; Freie Universität Berlin; Berlin Germany
- Institute for Immunology; Perelman School of Medicine; University of Pennsylvania; Philadelphia PA USA
| | - S. Rausch
- Institute of Immunology; Freie Universität Berlin; Berlin Germany
| | - K. Janek
- Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - A. Niewienda
- Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - A. Kühl
- Department of Pathology/Research Center ImmunoSciences (RCIS); Charité - Universitätsmedizin Berlin; Berlin Germany
| | - P. Henklein
- Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - R. Lucius
- Department of Molecular Parasitology; Humboldt-Universität; Berlin Germany
| | - E. Hamelmann
- Ev. Hospital Bielefeld (EvKB); Children's Hospital; Bielefeld Germany
| | - S. Hartmann
- Institute of Immunology; Freie Universität Berlin; Berlin Germany
| |
Collapse
|
12
|
Hovestädt M, Kuckelkorn U, Niewienda A, Keller C, Goede A, Ay B, Günther S, Janek K, Volkmer R, Holzhütter HG. Rapid degradation of solid-phase bound peptides by the 20S proteasome. J Pept Sci 2013; 19:588-97. [DOI: 10.1002/psc.2536] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Marc Hovestädt
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Ulrike Kuckelkorn
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Agathe Niewienda
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Christin Keller
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Andrean Goede
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Bernhard Ay
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics Group, Institute of Pharmaceutical Sciences; Albert-Ludwigs-University Freiburg; Freiburg Germany
| | - Katharina Janek
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Rudolf Volkmer
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Hermann-Georg Holzhütter
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| |
Collapse
|
13
|
Mishto M, Goede A, Taube KT, Keller C, Janek K, Henklein P, Niewienda A, Kloss A, Gohlke S, Dahlmann B, Enenkel C, Kloetzel PM. Driving forces of proteasome-catalyzed peptide splicing in yeast and humans. Mol Cell Proteomics 2012; 11:1008-23. [PMID: 22822185 DOI: 10.1074/mcp.m112.020164] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasome-catalyzed peptide splicing (PCPS) represents an additional activity of mammalian 20S proteasomes recently identified in connection with antigen presentation. We show here that PCPS is not restricted to mammalians but that it is also a feature of yeast 20S proteasomes catalyzed by all three active site β subunits. No major differences in splicing efficiency exist between human 20S standard- and immuno-proteasome or yeast 20S proteasome. Using H(2)(18)O to monitor the splicing reaction we also demonstrate that PCPS occurs via direct transpeptidation that slightly favors the generation of peptides spliced in cis over peptides spliced in trans. Splicing efficiency itself is shown to be controlled by proteasomal cleavage site preference as well as by the sequence characteristics of the spliced peptides. By use of kinetic data and quantitative analyses of PCPS obtained by mass spectrometry we developed a structural model with two PCPS binding sites in the neighborhood of the active Thr1.
Collapse
Affiliation(s)
- Michele Mishto
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Oudenarder Straβe 16, 13347 Berlin, Germany.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Habib SJ, Waizenegger T, Niewienda A, Paschen SA, Neupert W, Rapaport D. The N-terminal domain of Tob55 has a receptor-like function in the biogenesis of mitochondrial beta-barrel proteins. ACTA ACUST UNITED AC 2006; 176:77-88. [PMID: 17190789 PMCID: PMC2063629 DOI: 10.1083/jcb.200602050] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [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] [Indexed: 12/03/2022]
Abstract
β-Barrel proteins constitute a distinct class of mitochondrial outer membrane proteins. For import into mitochondria, their precursor forms engage the TOM complex. They are then relayed to the TOB complex, which mediates their insertion into the outer membrane. We studied the structure–function relationships of the core component of the TOB complex, Tob55. Tob55 precursors with deletions in the N-terminal domain were not affected in their targeting to and insertion into the mitochondrial outer membrane. Replacement of wild-type Tob55 by these deletion variants resulted in reduced growth of cells, and mitochondria isolated from such cells were impaired in their capacity to import β-barrel precursors. The purified N-terminal domain was able to bind β-barrel precursors in a specific manner. Collectively, these results demonstrate that the N-terminal domain of Tob55 recognizes precursors of β-barrel proteins. This recognition may contribute to the coupling of the translocation of β-barrel precursors across the TOM complex to their interaction with the TOB complex.
Collapse
Affiliation(s)
- Shukry J Habib
- Institut für Physiologische Chemie, Universität München, 81377 Munich, Germany
| | | | | | | | | | | |
Collapse
|