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Conforti JM, Ziegler AM, Worth CS, Nambiar AM, Bailey JT, Taube JH, Gallagher ES. Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques. bioRxiv 2024:2024.03.13.584881. [PMID: 38559195 PMCID: PMC10980087 DOI: 10.1101/2024.03.13.584881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. However, recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Thus, solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are detected and identified. We hypothesize that the mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. From these results, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.
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Affiliation(s)
- Jessica M. Conforti
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Amanda M. Ziegler
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Charli S. Worth
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Adhwaitha M. Nambiar
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Jacob T. Bailey
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Joseph H. Taube
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Elyssia S. Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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Sun Z, Huang M, Sokolowska I, Cao R, Chang K, Hu P, Mo J. Impact of Trisulfide on the Structure and Function of Different Antibody Constructs. J Pharm Sci 2023; 112:2637-2643. [PMID: 37595748 DOI: 10.1016/j.xphs.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/11/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Trisulfide is a post-translational modification (PTM) commonly found in recombinant antibodies. It has been demonstrated that trisulfide had no impact on the bioactivity of mono-specific antibodies (MsAbs). However, the impact of trisulfide on multi-specific antibodies has not been evaluated. In this study, two mass spectrometric methods were developed for comprehensive trisulfide characterization. The non-reduced peptide mapping method combined with the unique electron activated dissociation (EAD) provided signature fragments for confident trisulfide identification as well as trisulfide quantitation at individual sites. A higher throughput method using Fab mass analysis was also developed and qualified to support routine monitoring of trisulfide during process development. Fab mass analysis features simpler sample preparation and shorter analysis time but provides comparable results to the non-reduced peptide mapping method. In this study, a bi-specific (BsAb) and a tri-specific antibody (TsAb) were compared side-by-side with a MsAb to evaluate the impact of trisulfide on the structure and function of multi-specific antibodies. Results indicated that trisulfide dominantly formed at similar locations across different antibody constructs and had no impact on the size heterogeneity, charge heterogeneity, or bioactivities of any assessed antibodies. Together with the in vitro stability under heat stress (25 °C and 40 °C for up to four weeks) and rapid conversion from trisulfide to disulfide during in vivo circulation, trisulfide could be categorized as a non-critical quality attribute (non-CQA) for antibody products.
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Affiliation(s)
- Zhiyuan Sun
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA
| | - Maggie Huang
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA
| | - Izabela Sokolowska
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA
| | - Rui Cao
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA
| | - Kern Chang
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA
| | - Ping Hu
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA.
| | - Jingjie Mo
- Analytical Development, Discovery, Product Development & Supply, Janssen Research & Development, LLC, Malvern, PA 19355, USA.
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Le SB, Nordborg A, Josefsen KD, Olsen SM, Sletta H. Cultivation of Mycolicibacterium spp. Mutants in Miniaturized and High-Throughput Format to Characterize Their Growth, Phytosterol Conversion Ability, and Resistance to the Steroid Products. Methods Mol Biol 2023; 2704:185-200. [PMID: 37642845 DOI: 10.1007/978-1-0716-3385-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 08/31/2023]
Abstract
This chapter describes methods for cultivation and characterization of the growth of Mycolicibacterium spp. mutants in a microbioreactor system in the presence of steroids and/or phytosterols followed by high-throughput mass spectrometry analysis to describe their ability to convert phytosterols into the target steroid androstenedione (AD). We focus on Mycolicibacterium neoaurum NRRL B-3805 ΔkstD which can convert phytosterol into androstenedione (AD) as one of its major steroid products, and mutants thereof with increased tolerance towards this end-product. By using BioLector 48-well plates with optodes at the bottom of each well, bacterial growth can be monitored online despite the turbidity of the growth medium resulting from non-dissolved phytosterol and steroid particles. To cope with the large number of samples that accumulate during growth experiments in microbioreactors and similar formats (e.g., microtiter plates), protocols for extraction and subsequent RapidFire-MS analysis are presented. This reduces the analysis time per sample to 10 s from 10 min required for regular LC-MS analysis.
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Affiliation(s)
- Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Nordborg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway.
| | | | - Silje Malene Olsen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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Song L, Chen J, Sun A, Schekman R. APEX-mediated Proximity Labeling of Proteins in Cells Targeted by Extracellular Vesicles. Bio Protoc 2021; 11:e4213. [PMID: 34859128 DOI: 10.21769/bioprotoc.4213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/28/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) are thought to mediate intercellular communication through the delivery of cargo proteins and RNA to target cells. The uptake of EVs is often followed visually using lipophilic-dyes or fluorescently-tagged proteins to label membrane constituents that are then internalized into recipient cells ( Christianson et al., 2013 ; De Jong et al., 2019 ). However, these methods do not probe the exposure of EV cargo to intracellular compartments, such as the cytoplasm and nucleus, where protein or RNA molecules could elicit functional changes in recipient cells. In this protocol, we employ an EV cargo protein-APEX fusion to detect proximity interactions with recipient cell cytoplasmic/nuclear targets. This approach results in the biotinylation of proteins in close contact with the reporter fusion and thus permits profiling of biotinylated proteins affinity purified on immobilized streptavidin beads. Graphic abstract: Schematic showing three steps of APEX-mediated proximity labeling of proteins in cells targeted by EVs.
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Affiliation(s)
- Lu Song
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jun Chen
- California Institute for Quantitative Biosciences at UC Berkeley (QB3-Berkeley), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Angela Sun
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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Hanrieder J. Preface: Mass spectrometry in Alzheimer disease: This is the Preface for the special issue "Mass Spectrometry in Alzheimer Disease". J Neurochem 2021; 159:207-210. [PMID: 34665876 DOI: 10.1111/jnc.15512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
This preface introduces the content of the special issue on 'Mass Spectrometry in Alzheimer Disease'. Here, an overview is provided on how mass spectrometry is contributing to a broader understanding of AD pathobiology. Mass spectrometry has become a major technology in biomedical analysis and research. This includes biochemical and clinical studies that aim to detail our understanding of Alzheimer disease pathogenesis and pathobiology (AD). In this special issue, key experts in the field present exciting developments and applications of MS in the context of studying AD pathology. These studies span from basic biochemical and neuropathological studies, over advanced metabolomics- and proteomics, towards comprehensive biomarker studies, as well as more recently, in situ mass spectrometry-based imaging (MSI). Together, these studies highlight the key relevance of current and emerging MS technologies to detect, delineate and understand principle pathogenic mechanisms underlying AD.
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Affiliation(s)
- Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
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Khan MM, Välikangas T, Khan MH, Moulder R, Ullah U, Bhosale SD, Komsi E, Butt U, Qiao X, Westermarck J, Elo LL, Lahesmaa R. Protein interactome of the Cancerous Inhibitor of protein phosphatase 2A (CIP2A) in Th17 cells. Curr Res Immunol 2020; 1:10-22. [PMID: 33817627 PMCID: PMC8008788 DOI: 10.1016/j.crimmu.2020.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 10/08/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Cancerous inhibitor of protein phosphatase 2A (CIP2A) is involved in immune response, cancer progression, and Alzheimer's disease. However, an understanding of the mechanistic basis of its function in this wide spectrum of physiological and pathological processes is limited due to its poorly characterized interaction networks. Here we present the first systematic characterization of the CIP2A interactome by affinity-purification mass spectrometry combined with validation by selected reaction monitoring targeted mass spectrometry (SRM-MS) analysis in T helper (Th) 17 (Th17) cells. In addition to the known regulatory subunits of protein phosphatase 2A (PP2A), the catalytic subunits of protein PP2A were found to be interacting with CIP2A. Furthermore, the regulatory (PPP1R18, and PPP1R12A) and catalytic (PPP1CA) subunits of phosphatase PP1 were identified among the top novel CIP2A interactors. Evaluation of the ontologies associated with the proteins in this interactome revealed that they were linked with RNA metabolic processing and splicing, protein traffic, cytoskeleton regulation and ubiquitin-mediated protein degradation processes. Taken together, this network of protein-protein interactions will be important for understanding and further exploring the biological processes and mechanisms regulated by CIP2A both in physiological and pathological conditions. The first characterisation of the CIP2A interactome in Th17 cells. Key interactions validated by targeted SRM-MS proteomics, western blot and confocal microscopy. Pathway analysis of the interactome revealed interrelationships with proteins across a broad range of cellular processes. The study identifies for the first time the interaction of phosphatase PP1 with CIP2A.
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Affiliation(s)
- Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM), Medical Faculty, University of Turku, Turku, Finland
| | - Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Doctoral Programme in Mathematics and Computer Sciences (MATTI), University of Turku, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ubaid Ullah
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh Dilip Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM), Medical Faculty, University of Turku, Turku, Finland
| | - Elina Komsi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Umar Butt
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Xi Qiao
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Corresponding author. Turku Bioscience Centre, Tykistökatu 6A, Turku, 20520, Finland.
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Santana H, Espinosa LA, Sánchez A, Bolaño Alvarez A, Besada V, González LJ. Mass spectrometric and kinetics characterization of modified species of Growth Hormone Releasing Hexapeptide generated under thermal stress in different pH and buffers. J Pharm Biomed Anal 2021; 194:113776. [PMID: 33272786 DOI: 10.1016/j.jpba.2020.113776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022]
Abstract
Growth Hormone Releasing Peptide-6 (GHRP-6) is a promising molecule (H-His1-d-Trp- Ala-Trp-d-Phe-Lys6-NH2) for the treatment of several diseases. Studies on the degradation pathways of this molecule under stressed conditions are needed to develop appropriate formulations. Degradation products (DPs) of GHRP-6, generated by heating in the dark at 60 °C with pH ranging from 3.0 to 8.0 and in presence of common buffers, were isolated by RP-HPLC and characterized by ESI-MS/MS. C-terminal deamidation of GHRP-6 was generated preferentially at pH 3.0 and 8.0. Hydrolysis and head-to-tail cyclization were favored at pH ranging from 6.0 to 7.0 in phosphate containing buffers. A DP with +12 Da molecular mass was presumably originated by the reaction with formaldehyde derived from some of the additives and/or elastomeric closures. Certain DPs derived from the acylation reaction of the tri- and di-carboxylic buffering species were favored at pH 3.0-6.0 and indicate that buffer components, including those "Generally Recognized as Safe", may potentially introduce chemical modifications and product heterogeneity. Nano LC-MS/MS analysis revealed GHRP-6 was also detected as a low-abundance species with Trp oxidized to 5-hydroxy, kynurenine, and N-formylkynurenine. The kinetics for the formation of the major degradation products was also studied by RP-HPLC.
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Świądro M, Stelmaszczyk P, Wietecha-Posłuszny R, Dudek D. Development of a new method for drug detection based on a combination of the dried blood spot method and capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122339. [PMID: 32877802 DOI: 10.1016/j.jchromb.2020.122339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 02/02/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022]
Abstract
The aim of this study was to develop a new approach to sample preparation of biological material based on a combination of the Dried Blood Spot (DBS) method and capillary electrophoresis coupled with mass spectrometry (CE-MS) for the analysis of blood samples collected in vivo or post-mortem. The proposed approach allowed the identification of typical drugs from different groups, such as tricyclic antidepressants (amitriptyline, imipramine), selective serotonin reuptake inhibitors (citalopram), benzodiazepines (tetrazepam) and hypnotics (zolpidem). In this study, a blood sample was spotted on FTA DMPK C cards, then dried, and 6-mm discs were cut out. The sample preparation procedure involved microwave-assisted extraction (MAE). Various extraction agents, temperatures and durations of extraction were examined in order to achieve the highest efficiency of the process. The method was subjected to a validation procedure. Limits of detection (LOD = 1.76 - 14.7 ng/mL) and quantification (LOQ = 5.25 - 49.0 ng/mL), inter- (CV = 1.31 - 9.43%) and intra- (CV = 3.26 - 18.52%) day precision of the determinations, recovery (RE = 85.0-105.4%) and matrix effect on ionization of analytes (ME = 98.6-105.5%) were determined. Furthermore, the developed DBS/MAE/CM-MS method was selective and analytes present in the blood applied on DBS cards were found to be stable after 7 and after 14 days. Moreover, the developed method was successfully applied to the analysis of both post-mortem samples and blood samples taken from patients treated with the analyzed drugs.
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Affiliation(s)
- Magdalena Świądro
- Laboratory for Forensic Chemistry, Department of Analytical Chemistry, Faculty of Chemistry, Jagiellonian University, 2, Gronostajowa St., 30-387 Kraków, Poland
| | - Paweł Stelmaszczyk
- Laboratory for Forensic Chemistry, Department of Analytical Chemistry, Faculty of Chemistry, Jagiellonian University, 2, Gronostajowa St., 30-387 Kraków, Poland
| | - Renata Wietecha-Posłuszny
- Laboratory for Forensic Chemistry, Department of Analytical Chemistry, Faculty of Chemistry, Jagiellonian University, 2, Gronostajowa St., 30-387 Kraków, Poland.
| | - Dominika Dudek
- Department of Adult Psychiatry, Jagiellonian University Medical College, 21a, Mikołaja Kopernika St., 31-000 Kraków, Poland
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Abstract
Transcription machinery plays a central role in both the gene expression and nucleoid compaction. In this chapter we elaborate on the optimization of RNA polymerase purification protocol using a mild procedure with the purpose of preserving its native composition. This protocol combines protein extraction under non-denaturing conditions, heparin based affinity purification, and consequent BN-PAGE-SDS-PAGE separation. The outcome is an experimental procedure for screening RNA polymerase composition with associated proteins, in various bacterial strains or mutant backgrounds. With modifications in the column purification step, this procedure can be applied for isolation and identification of the components of other multi-protein complexes.
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Affiliation(s)
- Sanja Mehandziska
- School of Engineering and Science, Jacobs University Bremen, 28759, Bremen, Germany
| | - Alexander M Petrescu
- School of Engineering and Science, Jacobs University Bremen, 28759, Bremen, Germany
| | - Georgi Muskhelishvili
- School of Engineering and Science, Jacobs University Bremen, 28759, Bremen, Germany.
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10
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Li Z, Moniz H, Wang S, Ramiah A, Zhang F, Moremen KW, Linhardt RJ, Sharp JS. High structural resolution hydroxyl radical protein footprinting reveals an extended Robo1-heparin binding interface. J Biol Chem 2015; 290:10729-40. [PMID: 25752613 PMCID: PMC4409239 DOI: 10.1074/jbc.m115.648410] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/05/2015] [Indexed: 11/06/2022] Open
Abstract
Interaction of transmembrane receptors of the Robo family and the secreted protein Slit provides important signals in the development of the central nervous system and regulation of axonal midline crossing. Heparan sulfate, a sulfated linear polysaccharide modified in a complex variety of ways, serves as an essential co-receptor in Slit-Robo signaling. Previous studies have shown that closely related heparin octasaccharides bind to Drosophila Robo directly, and surface plasmon resonance analysis revealed that Robo1 binds more tightly to full-length unfractionated heparin. For the first time, we utilized electron transfer dissociation-based high spatial resolution hydroxyl radical protein footprinting to identify two separate binding sites for heparin interaction with Robo1: one binding site at the previously identified site for heparin dp8 and a second binding site at the N terminus of Robo1 that is disordered in the x-ray crystal structure. Mutagenesis of the identified N-terminal binding site exhibited a decrease in binding affinity as measured by surface plasmon resonance and heparin affinity chromatography. Footprinting also indicated that heparin binding induces a minor change in the conformation and/or dynamics of the Ig2 domain, but no major conformational changes were detected. These results indicate a second low affinity binding site in the Robo-Slit complex as well as suggesting the role of the Ig2 domain of Robo1 in heparin-mediated signal transduction. This study also marks the first use of electron transfer dissociation-based high spatial resolution hydroxyl radical protein footprinting, which shows great utility for the characterization of protein-carbohydrate complexes.
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Affiliation(s)
- Zixuan Li
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
| | - Heather Moniz
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
| | - Shuo Wang
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
| | - Annapoorani Ramiah
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
| | - Fuming Zhang
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Kelley W Moremen
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
| | - Robert J Linhardt
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Joshua S Sharp
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602 and
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11
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Deng X, Walker RG, Morris J, Davidson WS, Thompson TB. Role of Conserved Proline Residues in Human Apolipoprotein A-IV Structure and Function. J Biol Chem 2015; 290:10689-702. [PMID: 25733664 PMCID: PMC4409236 DOI: 10.1074/jbc.m115.637058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/23/2015] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein (apo)A-IV is a lipid emulsifying protein linked to a range of protective roles in obesity, diabetes, and cardiovascular disease. It exists in several states in plasma including lipid-bound in HDL and chylomicrons and as monomeric and dimeric lipid-free/poor forms. Our recent x-ray crystal structure of the central domain of apoA-IV shows that it adopts an elongated helical structure that dimerizes via two long reciprocating helices. A striking feature is the alignment of conserved proline residues across the dimer interface. We speculated that this plays important roles in the structure of the lipid-free protein and its ability to bind lipid. Here we show that the systematic conversion of these prolines to alanine increased the thermodynamic stability of apoA-IV and its propensity to oligomerize. Despite the structural stabilization, we noted an increase in the ability to bind and reorganize lipids and to promote cholesterol efflux from cells. The novel properties of these mutants allowed us to isolate the first trimeric form of an exchangeable apolipoprotein and characterize it by small-angle x-ray scattering and chemical cross-linking. The results suggest that the reciprocating helix interaction is a common feature of all apoA-IV oligomers. We propose a model of how self-association of apoA-IV can result in spherical lipoprotein particles, a model that may have broader applications to other exchangeable apolipoprotein family members.
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Affiliation(s)
- Xiaodi Deng
- From the Departments of Molecular Genetics, Biochemistry and Microbiology and
| | - Ryan G Walker
- From the Departments of Molecular Genetics, Biochemistry and Microbiology and
| | - Jamie Morris
- Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237
| | - W Sean Davidson
- Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237
| | - Thomas B Thompson
- From the Departments of Molecular Genetics, Biochemistry and Microbiology and
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12
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Carlson SM, Moore KE, Sankaran SM, Reynoird N, Elias JE, Gozani O. A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme. J Biol Chem 2015; 290:12040-7. [PMID: 25795785 DOI: 10.1074/jbc.m115.641530] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 01/27/2015] [Indexed: 11/06/2022] Open
Abstract
The lysine methyltransferase (KMT) SETMAR is implicated in the response to and repair of DNA damage, but its molecular function is not clear. SETMAR has been associated with dimethylation of histone H3 lysine 36 (H3K36) at sites of DNA damage. However, SETMAR does not methylate H3K36 in vitro. This and the observation that SETMAR is not active on nucleosomes suggest that H3K36 methylation is not a physiologically relevant activity. To identify potential non-histone substrates, we utilized a strategy on the basis of quantitative proteomic analysis of methylated lysine. Our approach identified lysine 130 of the mRNA splicing factor snRNP70 as a SETMAR substrate in vitro, and we show that the enzyme primarily generates monomethylation at this position. Furthermore, we show that SETMAR methylates snRNP70 Lys-130 in cells. Because snRNP70 is a key early regulator of 5' splice site selection, our results suggest a model in which methylation of snRNP70 by SETMAR regulates constitutive and/or alternative splicing. In addition, the proteomic strategy described here is broadly applicable and is a promising route for large-scale mapping of KMT substrates.
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Affiliation(s)
| | - Kaitlyn E Moore
- From the Department of Biology and Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305
| | | | | | - Joshua E Elias
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305
| | - Or Gozani
- From the Department of Biology and ogozani@stanfordedu
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13
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Batchu KC, Hokynar K, Jeltsch M, Mattonet K, Somerharju P. Substrate efflux propensity is the key determinant of Ca2+-independent phospholipase A-β (iPLAβ)-mediated glycerophospholipid hydrolysis. J Biol Chem 2015; 290:10093-103. [PMID: 25713085 DOI: 10.1074/jbc.m115.642835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 02/05/2015] [Indexed: 12/13/2022] Open
Abstract
The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca(2+)-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated.
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Affiliation(s)
| | - Kati Hokynar
- From the Departments of Biochemistry and Developmental Biology and
| | - Michael Jeltsch
- Biomedicine, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Kenny Mattonet
- Biomedicine, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
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14
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Setiaputra D, Ross JD, Lu S, Cheng DT, Dong MQ, Yip CK. Conformational flexibility and subunit arrangement of the modular yeast Spt-Ada-Gcn5 acetyltransferase complex. J Biol Chem 2015; 290:10057-70. [PMID: 25713136 DOI: 10.1074/jbc.m114.624684] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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: 11/12/2014] [Indexed: 01/28/2023] Open
Abstract
The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility.
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Affiliation(s)
- Dheva Setiaputra
- From the Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - James D Ross
- From the Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - Shan Lu
- the National Institute of Biological Sciences, Beijing 102206, China
| | - Derrick T Cheng
- From the Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - Meng-Qiu Dong
- the National Institute of Biological Sciences, Beijing 102206, China
| | - Calvin K Yip
- From the Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
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15
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Stäubert C, Bhuiyan H, Lindahl A, Broom OJ, Zhu Y, Islam S, Linnarsson S, Lehtiö J, Nordström A. Rewired metabolism in drug-resistant leukemia cells: a metabolic switch hallmarked by reduced dependence on exogenous glutamine. J Biol Chem 2015; 290:8348-59. [PMID: 25697355 DOI: 10.1074/jbc.m114.618769] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cancer cells that escape induction therapy are a major cause of relapse. Understanding metabolic alterations associated with drug resistance opens up unexplored opportunities for the development of new therapeutic strategies. Here, we applied a broad spectrum of technologies including RNA sequencing, global untargeted metabolomics, and stable isotope labeling mass spectrometry to identify metabolic changes in P-glycoprotein overexpressing T-cell acute lymphoblastic leukemia (ALL) cells, which escaped a therapeutically relevant daunorubicin treatment. We show that compared with sensitive ALL cells, resistant leukemia cells possess a fundamentally rewired central metabolism characterized by reduced dependence on glutamine despite a lack of expression of glutamate-ammonia ligase (GLUL), a higher demand for glucose and an altered rate of fatty acid β-oxidation, accompanied by a decreased pantothenic acid uptake capacity. We experimentally validate our findings by selectively targeting components of this metabolic switch, using approved drugs and starvation approaches followed by cell viability analyses in both the ALL cells and in an acute myeloid leukemia (AML) sensitive/resistant cell line pair. We demonstrate how comparative metabolomics and RNA expression profiling of drug-sensitive and -resistant cells expose targetable metabolic changes and potential resistance markers. Our results show that drug resistance is associated with significant metabolic costs in cancer cells, which could be exploited using new therapeutic strategies.
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Affiliation(s)
- Claudia Stäubert
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden, the Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden, the Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Hasanuzzaman Bhuiyan
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Anna Lindahl
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Oliver Jay Broom
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
| | - Yafeng Zhu
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Saiful Islam
- the Departments of Medical Biochemistry and Biophysics and
| | | | - Janne Lehtiö
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Anders Nordström
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden, the Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden, Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
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16
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Corradini E, Burgers PP, Plank M, Heck AJR, Scholten A. Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform. J Biol Chem 2015; 290:7887-96. [PMID: 25653285 DOI: 10.1074/jbc.m114.622613] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions are important in providing compartmentalization and specificity in cellular signal transduction. Many studies have hallmarked the well designed compartmentalization of the cAMP-dependent protein kinase (PKA) through its anchoring proteins. Much less data are available on the compartmentalization of its closest homolog, cGMP-dependent protein kinase (PKG), via its own PKG anchoring proteins (GKAPs). For the enrichment, screening, and discovery of (novel) PKA anchoring proteins, a plethora of methodologies is available, including our previously described chemical proteomics approach based on immobilized cAMP or cGMP. Although this method was demonstrated to be effective, each immobilized cyclic nucleotide did not discriminate in the enrichment for either PKA or PKG and their secondary interactors. Hence, with PKG signaling components being less abundant in most tissues, it turned out to be challenging to enrich and identify GKAPs. Here we extend this cAMP-based chemical proteomics approach using competitive concentrations of free cyclic nucleotides to isolate each kinase and its secondary interactors. Using this approach, we identified Huntingtin-associated protein 1 (HAP1) as a putative novel GKAP. Through sequence alignment with known GKAPs and secondary structure prediction analysis, we defined a small sequence domain mediating the interaction with PKG Iβ but not PKG Iα. In vitro binding studies and site-directed mutagenesis further confirmed the specificity and affinity of HAP1 binding to the PKG Iβ N terminus. These data fully support that HAP1 is a GKAP, anchoring specifically to the cGMP-dependent protein kinase isoform Iβ, and provide further evidence that also PKG spatiotemporal signaling is largely controlled by anchoring proteins.
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Affiliation(s)
- Eleonora Corradini
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pepijn P Burgers
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Michael Plank
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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17
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Hudson DM, Joeng KS, Werther R, Rajagopal A, Weis M, Lee BH, Eyre DR. Post-translationally abnormal collagens of prolyl 3-hydroxylase-2 null mice offer a pathobiological mechanism for the high myopia linked to human LEPREL1 mutations. J Biol Chem 2015; 290:8613-22. [PMID: 25645914 DOI: 10.1074/jbc.m114.634915] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myopia, the leading cause of visual impairment worldwide, results from an increase in the axial length of the eyeball. Mutations in LEPREL1, the gene encoding prolyl 3-hydroxylase-2 (P3H2), have recently been identified in individuals with recessively inherited nonsyndromic severe myopia. P3H2 is a member of a family of genes that includes three isoenzymes of prolyl 3-hydroxylase (P3H), P3H1, P3H2, and P3H3. Fundamentally, it is understood that P3H1 is responsible for converting proline to 3-hydroxyproline. This limited additional knowledge also suggests that each isoenzyme has evolved different collagen sequence-preferred substrate specificities. In this study, differences in prolyl 3-hydroxylation were screened in eye tissues from P3h2-null (P3h2(n/n)) and wild-type mice to seek tissue-specific effects due the lack of P3H2 activity on post-translational collagen chemistry that could explain myopia. The mice were viable and had no gross musculoskeletal phenotypes. Tissues from sclera and cornea (type I collagen) and lens capsule (type IV collagen) were dissected from mouse eyes, and multiple sites of prolyl 3-hydroxylation were identified by mass spectrometry. The level of prolyl 3-hydroxylation at multiple substrate sites from type I collagen chains was high in sclera, similar to tendon. Almost every known site of prolyl 3-hydroxylation in types I and IV collagen from P3h2(n/n) mouse eye tissues was significantly under-hydroxylated compared with their wild-type littermates. We conclude that altered collagen prolyl 3-hydroxylation is caused by loss of P3H2. We hypothesize that this leads to structural abnormalities in multiple eye tissues, but particularly sclera, causing progressive myopia.
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Affiliation(s)
- David M Hudson
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195 and
| | - Kyu Sang Joeng
- the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Rachel Werther
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195 and
| | - Abbhirami Rajagopal
- the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - MaryAnn Weis
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195 and
| | - Brendan H Lee
- the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - David R Eyre
- From the Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington 98195 and
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18
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Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA, Clarke CF. Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. J Biol Chem 2015; 290:7517-34. [PMID: 25631044 DOI: 10.1074/jbc.m114.633131] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [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: 01/01/2023] Open
Abstract
Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1-COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. Here, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11.
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Affiliation(s)
- Christopher M Allan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Agape M Awad
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Jarrett S Johnson
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Dyna I Shirasaki
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Charles Wang
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Crysten E Blaby-Haas
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Sabeeha S Merchant
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, the UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Joseph A Loo
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, the Department of Biological Chemistry, and the UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Catherine F Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute,
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19
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Smith AD, Wilks A. Differential contributions of the outer membrane receptors PhuR and HasR to heme acquisition in Pseudomonas aeruginosa. J Biol Chem 2015; 290:7756-66. [PMID: 25616666 DOI: 10.1074/jbc.m114.633495] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa PAO1 encodes two outer membrane receptors, PhuR (Pseudomonas heme uptake) and HasR (heme assimilation system). The HasR and PhuR receptors have distinct heme coordinating ligands and substrate specificities. HasR is encoded in an operon with a secreted hemophore, HasAp. In contrast the non-hemophore-dependent PhuR is encoded within an operon along with proteins required for heme translocation into the cytoplasm. Herein we report on the contributions of the HasR and PhuR receptors to heme uptake and utilization. Employing bacterial genetics and isotopic [(13)C]heme labeling studies we have shown both PhuR and HasR are required for optimal heme utilization. However, the unique His-Tyr-ligated PhuR plays a major role in the acquisition of heme. In contrast the HasR receptor plays a primary role in the sensing of extracellular heme and a supplementary role in heme uptake. We propose PhuR and HasR represent non-redundant heme receptors, capable of accessing heme across a wide range of physiological conditions on colonization of the host.
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Affiliation(s)
- Aaron D Smith
- From the Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Angela Wilks
- From the Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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20
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Zhao H, Chiaro CR, Zhang L, Smith PB, Chan CY, Pedley AM, Pugh RJ, French JB, Patterson AD, Benkovic SJ. Quantitative analysis of purine nucleotides indicates that purinosomes increase de novo purine biosynthesis. J Biol Chem 2015; 290:6705-13. [PMID: 25605736 DOI: 10.1074/jbc.m114.628701] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enzymes in the de novo purine biosynthesis pathway are recruited to form a dynamic metabolic complex referred to as the purinosome. Previous studies have demonstrated that purinosome assembly responds to purine levels in culture medium. Purine-depleted medium or 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole (DMAT) treatment stimulates the purinosome assembly in HeLa cells. Here, several metabolomic technologies were applied to quantify the static cellular levels of purine nucleotides and measure the de novo biosynthesis rate of IMP, AMP, and GMP. Direct comparison of purinosome-rich cells (cultured in purine-depleted medium) and normal cells showed a 3-fold increase in IMP concentration in purinosome-rich cells and similar levels of AMP, GMP, and ratios of AMP/GMP and ATP/ADP for both. In addition, a higher level of IMP was also observed in HeLa cells treated with DMAT. Furthermore, increases in the de novo IMP/AMP/GMP biosynthetic flux rate under purine-depleted condition were observed. The synthetic enzymes, adenylosuccinate synthase (ADSS) and inosine monophosphate dehydrogenase (IMPDH), downstream of IMP were also shown to be part of the purinosome. Collectively, these results provide further evidence that purinosome assembly is directly related to activated de novo purine biosynthesis, consistent with the functionality of the purinosome.
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Affiliation(s)
| | | | - Limin Zhang
- Metabolomics Facility, Center for Molecular Toxicology and Carcinogenesis, and the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS), Wuhan 430071, China, and
| | - Philip B Smith
- Metabolomics Facility, Center for Molecular Toxicology and Carcinogenesis, and
| | - Chung Yu Chan
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | | | | | - Jarrod B French
- the Departments of Biochemistry and Cell Biology and Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Andrew D Patterson
- Metabolomics Facility, Center for Molecular Toxicology and Carcinogenesis, and
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21
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Gordon ON, Luis PB, Sintim HO, Schneider C. Unraveling curcumin degradation: autoxidation proceeds through spiroepoxide and vinylether intermediates en route to the main bicyclopentadione. J Biol Chem 2015; 290:4817-4828. [PMID: 25564617 DOI: 10.1074/jbc.m114.618785] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Curcumin is a dietary anti-inflammatory and chemopreventive agent consisting of two methoxyphenol rings connected by a conjugated heptadienedione chain. Curcumin is unstable at physiological pH and rapidly degrades in an autoxidation reaction to a major bicyclopentadione product in which the 7-carbon chain has undergone oxygenation and double cyclization. Early degradation products (but not the final bicyclopentadione) mediate topoisomerase poisoning and possibly many other activities of curcumin, but it is not known how many and what autoxidation products are formed, nor their mechanism of formation. Here, using [(14)C2]curcumin as a tracer, seven novel autoxidation products, including two reaction intermediates, were isolated and identified using one- and two-dimensional NMR and mass spectrometry. The unusual spiroepoxide and vinylether reaction intermediates are precursors to the final bicyclopentadione product. A mechanism for the autoxidation of curcumin is proposed that accounts for the addition and exchange of oxygen that have been determined using (18)O2 and H2(18)O. Several of the by-products are formed from an endoperoxide intermediate via reactions that are well precedented in lipid peroxidation. The electrophilic spiroepoxide intermediate formed a stable adduct with N-acetylcysteine, suggesting that oxidative transformation is required for biological effects mediated by covalent adduction to protein thiols. The spontaneous autoxidation distinguishes curcumin among natural polyphenolic compounds of therapeutic interest; the formation of chemically diverse reactive and electrophilic products provides a novel paradigm for understanding the polypharmacological effects of curcumin.
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Affiliation(s)
- Odaine N Gordon
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, Tennessee 37232 and
| | - Paula B Luis
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, Tennessee 37232 and
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Claus Schneider
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, Tennessee 37232 and.
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22
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Thomas MA, Buelow BJ, Nevins AM, Jones SE, Peterson FC, Gundry RL, Grayson MH, Volkman BF. Structure-function analysis of CCL28 in the development of post-viral asthma. J Biol Chem 2015; 290:4528-36. [PMID: 25556652 DOI: 10.1074/jbc.m114.627786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CCL28 is a human chemokine constitutively expressed by epithelial cells in diverse mucosal tissues and is known to attract a variety of immune cell types including T-cell subsets and eosinophils. Elevated levels of CCL28 have been found in the airways of individuals with asthma, and previous studies have indicated that CCL28 plays a vital role in the acute development of post-viral asthma. Our study builds on this, demonstrating that CCL28 is also important in the chronic post-viral asthma phenotype. In the absence of a viral infection, we also demonstrate that CCL28 is both necessary and sufficient for induction of asthma pathology. Additionally, we present the first effort aimed at elucidating the structural features of CCL28. Chemokines are defined by a conserved tertiary structure composed of a three-stranded β-sheet and a C-terminal α-helix constrained by two disulfide bonds. In addition to the four disulfide bond-forming cysteine residues that define the traditional chemokine fold, CCL28 possesses two additional cysteine residues that form a third disulfide bond. If all disulfide bonds are disrupted, recombinant human CCL28 is no longer able to drive mouse CD4+ T-cell chemotaxis or in vivo airway hyper-reactivity, indicating that the conserved chemokine fold is necessary for its biologic activity. Due to the intimate relationship between CCL28 and asthma pathology, it is clear that CCL28 presents a novel target for the development of alternative asthma therapeutics.
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Affiliation(s)
- Monica A Thomas
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Becky J Buelow
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Amanda M Nevins
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Stephanie E Jones
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Francis C Peterson
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Rebekah L Gundry
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Mitchell H Grayson
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Brian F Volkman
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
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23
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Nordén R, Halim A, Nyström K, Bennett EP, Mandel U, Olofsson S, Nilsson J, Larson G. O-linked glycosylation of the mucin domain of the herpes simplex virus type 1-specific glycoprotein gC-1 is temporally regulated in a seed-and-spread manner. J Biol Chem 2014; 290:5078-5091. [PMID: 25548287 DOI: 10.1074/jbc.m114.616409] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The herpes simplex virus type 1 (HSV-1) glycoprotein gC-1, participating in viral receptor interactions and immunity interference, harbors a mucin-like domain with multiple clustered O-linked glycans. Using HSV-1-infected diploid human fibroblasts, an authentic target for HSV-1 infection, and a protein immunoaffinity procedure, we enriched fully glycosylated gC-1 and a series of its biosynthetic intermediates. This fraction was subjected to trypsin digestion and a LC-MS/MS glycoproteomics approach. In parallel, we characterized the expression patterns of the 20 isoforms of human GalNAc transferases responsible for initiation of O-linked glycosylation. The gC-1 O-glycosylation was regulated in an orderly manner initiated by synchronous addition of one GalNAc unit each to Thr-87 and Thr-91 and one GalNAc unit to either Thr-99 or Thr-101, forming a core glycopeptide for subsequent additions of in all 11 GalNAc residues to selected Ser and Thr residues of the Thr-76-Lys-107 stretch of the mucin domain. The expression patterns of GalNAc transferases in the infected cells suggested that initial additions of GalNAc were carried out by initiating GalNAc transferases, in particular GalNAc-T2, whereas subsequent GalNAc additions were carried out by followup transferases, in particular GalNAc-T10. Essentially all of the susceptible Ser or Thr residues had to acquire their GalNAc units before any elongation to longer O-linked glycans of the gC-1-associated GalNAc units was permitted. Because the GalNAc occupancy pattern is of relevance for receptor binding of gC-1, the data provide a model to delineate biosynthetic steps of O-linked glycosylation of the gC-1 mucin domain in HSV-1-infected target cells.
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Affiliation(s)
- Rickard Nordén
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and; Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Kristina Nyström
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and
| | - Sigvard Olofsson
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden.
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24
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Walkup WG, Washburn L, Sweredoski MJ, Carlisle HJ, Graham RL, Hess S, Kennedy MB. Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases. J Biol Chem 2014; 290:4908-4927. [PMID: 25533468 DOI: 10.1074/jbc.m114.614420] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [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: 12/20/2022] Open
Abstract
synGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentrations in the postsynaptic density (PSD) fraction from the mammalian forebrain. We have previously shown that, in situ in the PSD fraction or in recombinant form in Sf9 cell membranes, synGAP is phosphorylated by Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), another prominent component of the PSD. Here, we show that recombinant synGAP (r-synGAP), lacking 102 residues at the N terminus, can be purified in soluble form and is phosphorylated by cyclin-dependent kinase 5 (CDK5) as well as by CaMKII. Phosphorylation of r-synGAP by CaMKII increases its HRas GAP activity by 25% and its Rap1 GAP activity by 76%. Conversely, phosphorylation by CDK5 increases r-synGAP's HRas GAP activity by 98% and its Rap1 GAP activity by 20%. Thus, phosphorylation by both kinases increases synGAP activity; CaMKII shifts the relative GAP activity toward inactivation of Rap1, and CDK5 shifts the relative activity toward inactivation of HRas. GAP activity toward Rap2 is not altered by phosphorylation by either kinase. CDK5 phosphorylates synGAP primarily at two sites, Ser-773 and Ser-802. Phosphorylation at Ser-773 inhibits r-synGAP activity, and phosphorylation at Ser-802 increases it. However, the net effect of concurrent phosphorylation of both sites, Ser-773 and Ser-802, is an increase in GAP activity. synGAP is phosphorylated at Ser-773 and Ser-802 in the PSD fraction, and its phosphorylation by CDK5 and CaMKII is differentially regulated by activation of NMDA-type glutamate receptors in cultured neurons.
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Affiliation(s)
| | | | - Michael J Sweredoski
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | | | - Robert L Graham
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Sonja Hess
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
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25
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Komaniecka I, Choma A, Mazur A, Duda KA, Lindner B, Schwudke D, Holst O. Occurrence of an unusual hopanoid-containing lipid A among lipopolysaccharides from Bradyrhizobium species. J Biol Chem 2014; 289:35644-55. [PMID: 25371196 PMCID: PMC4271246 DOI: 10.1074/jbc.m114.614529] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 09/26/2014] [Revised: 11/03/2014] [Indexed: 11/06/2022] Open
Abstract
The chemical structures of the unusual hopanoid-containing lipid A samples of the lipopolysaccharides (LPS) from three strains of Bradyrhizobium (slow-growing rhizobia) have been established. They differed considerably from other Gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. The structural details of this type of lipid A were established using one- and two-dimensional NMR spectroscopy, chemical composition analyses, and mass spectrometry techniques (electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry and MALDI-TOF-MS). In these lipid A samples the glucosamine disaccharide characteristic for enterobacterial lipid A was replaced by a 2,3-diamino-2,3-dideoxy-d-glucopyranosyl-(GlcpN3N) disaccharide, deprived of phosphate residues, and substituted by an α-d-Manp-(1→6)-α-d-Manp disaccharide substituting C-4' of the non-reducing (distal) GlcpN3N, and one residue of galacturonic acid (d-GalpA) α-(1→1)-linked to the reducing (proximal) amino sugar residue. Amide-linked 12:0(3-OH) and 14:0(3-OH) were identified. Some hydroxy groups of these fatty acids were further esterified by long (ω-1)-hydroxylated fatty acids comprising 26-34 carbon atoms. As confirmed by mass spectrometry techniques, these long chain fatty acids could form two or three acyloxyacyl residues. The triterpenoid derivatives were identified as 34-carboxyl-bacteriohopane-32,33-diol and 34-carboxyl-2β-methyl-bacteriohopane-32,33-diol and were covalently linked to the (ω-1)-hydroxy group of very long chain fatty acid in bradyrhizobial lipid A. Bradyrhizobium japonicum possessed lipid A species with two hopanoid residues.
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Affiliation(s)
- Iwona Komaniecka
- From the Department of Genetics and Microbiology, Maria Curie-Sklodowska University, 20-033 Lublin and
| | - Adam Choma
- From the Department of Genetics and Microbiology, Maria Curie-Sklodowska University, 20-033 Lublin and
| | - Andrzej Mazur
- From the Department of Genetics and Microbiology, Maria Curie-Sklodowska University, 20-033 Lublin and
| | | | - Buko Lindner
- Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, 23845 Borstel, Poland
| | - Dominik Schwudke
- Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, 23845 Borstel, Poland
| | - Otto Holst
- the Divisions of Structural Biochemistry and
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26
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Hassan C, Chabrol E, Jahn L, Kester MGD, de Ru AH, Drijfhout JW, Rossjohn J, Falkenburg JHF, Heemskerk MHM, Gras S, van Veelen PA. Naturally processed non-canonical HLA-A*02:01 presented peptides. J Biol Chem 2014; 290:2593-603. [PMID: 25505266 DOI: 10.1074/jbc.m114.607028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [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: 01/01/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules generally present peptides (p) of 8 to 11 amino acids (aa) in length. Although an increasing number of examples with lengthy (>11 aa) peptides, presented mostly by HLA-B alleles, have been reported. Here we characterize HLA-A*02:01 restricted, in addition to the HLA-B*0702 and HLA-B*4402 restricted, lengthy peptides (>11 aa) arising from the B-cell ligandome. We analyzed a number of 15-mer peptides presented by HLA-A*02:01, and confirmed pHLA-I formation by HLA folding and thermal stability assays. Surprisingly the binding affinity and stability of the 15-mer epitopes in complex with HLA-A*02:01 were comparable with the values observed for canonical length (8 to 11 aa) HLA-A*02:01-restricted peptides. We solved the structures of two 15-mer epitopes in complex with HLA-A*02:01, within which the peptides adopted distinct super-bulged conformations. Moreover, we demonstrate that T-cells can recognize the 15-mer peptides in the context of HLA-A*02:01, indicating that these 15-mer peptides represent immunogenic ligands. Collectively, our data expand our understanding of longer epitopes in the context of HLA-I, highlighting that they are not limited to the HLA-B family, but can bind the ubiquitous HLA-A*02:01 molecule, and play an important role in T-cell immunity.
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Affiliation(s)
- Chopie Hassan
- From the Departments of Immunohematology and Blood Transfusion and
| | - Eric Chabrol
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia
| | - Lorenz Jahn
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Michel G D Kester
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arnoud H de Ru
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jan W Drijfhout
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
| | | | | | - Stephanie Gras
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and
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27
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Bulatov E, Martin EM, Chatterjee S, Knebel A, Shimamura S, Konijnenberg A, Johnson C, Zinn N, Grandi P, Sobott F, Ciulli A. Biophysical studies on interactions and assembly of full-size E3 ubiquitin ligase: suppressor of cytokine signaling 2 (SOCS2)-elongin BC-cullin 5-ring box protein 2 (RBX2). J Biol Chem 2014; 290:4178-91. [PMID: 25505247 PMCID: PMC4326827 DOI: 10.1074/jbc.m114.616664] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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] [Indexed: 01/10/2023] Open
Abstract
The multisubunit cullin RING E3 ubiquitin ligases (CRLs) target post-translationally modified substrates for ubiquitination and proteasomal degradation. The suppressors of cytokine signaling (SOCS) proteins play important roles in inflammatory processes, diabetes, and cancer and therefore represent attractive targets for therapeutic intervention. The SOCS proteins, among their other functions, serve as substrate receptors of CRL5 complexes. A member of the CRL family, SOCS2-EloBC-Cul5-Rbx2 (CRL5(SOCS2)), binds phosphorylated growth hormone receptor as its main substrate. Here, we demonstrate that the components of CRL5(SOCS2) can be specifically pulled from K562 human cell lysates using beads decorated with phosphorylated growth hormone receptor peptides. Subsequently, SOCS2-EloBC and full-length Cul5-Rbx2, recombinantly expressed in Escherichia coli and in Sf21 insect cells, respectively, were used to reconstitute neddylated and unneddylated CRL5(SOCS2) complexes in vitro. Finally, diverse biophysical methods were employed to study the assembly and interactions within the complexes. Unlike other E3 ligases, CRL5(SOCS2) was found to exist in a monomeric state as confirmed by size exclusion chromatography with inline multiangle static light scattering and native MS. Affinities of the protein-protein interactions within the multisubunit complex were measured by isothermal titration calorimetry. A structural model for full-size neddylated and unneddylated CRL5(SOCS2) complexes is supported by traveling wave ion mobility mass spectrometry data.
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Affiliation(s)
- Emil Bulatov
- From the Division of Biological Chemistry and Drug Discovery, College of Life Sciences, and the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Esther M Martin
- the Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium, and
| | - Sneha Chatterjee
- the Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium, and
| | - Axel Knebel
- the Medical Research Council Phosphorylation and Ubiquitylation Unit, College of Life Sciences, Sir James Black Center, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | | | - Albert Konijnenberg
- the Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium, and
| | - Clare Johnson
- the Medical Research Council Phosphorylation and Ubiquitylation Unit, College of Life Sciences, Sir James Black Center, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Nico Zinn
- Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paola Grandi
- Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Frank Sobott
- the Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium, and
| | - Alessio Ciulli
- From the Division of Biological Chemistry and Drug Discovery, College of Life Sciences, and the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom,
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28
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Monsellier E, Redeker V, Ruiz-Arlandis G, Bousset L, Melki R. Molecular interaction between the chaperone Hsc70 and the N-terminal flank of huntingtin exon 1 modulates aggregation. J Biol Chem 2014; 290:2560-76. [PMID: 25505179 DOI: 10.1074/jbc.m114.603332] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [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: 02/01/2023] Open
Abstract
The aggregation of polyglutamine (polyQ)-containing proteins is at the origin of nine neurodegenerative diseases. Molecular chaperones prevent the aggregation of polyQ-containing proteins. The exact mechanism by which they interact with polyQ-containing, aggregation-prone proteins and interfere with their assembly is unknown. Here we dissect the mechanism of interaction between a huntingtin exon 1 fragment of increasing polyQ lengths (HttEx1Qn), the aggregation of which is tightly associated with Huntington's disease, and molecular chaperone Hsc70. We show that Hsc70, together with its Hsp40 co-chaperones, inhibits HttEx1Qn aggregation and modifies the structural, seeding, and infectious properties of the resulting fibrils in a polyQ-independent manner. We demonstrate that Hsc70 binds the 17-residue-long N-terminal flank of HttEx1Qn, and we map Hsc70-HttEx1Qn surface interfaces at the residue level. Finally, we show that this interaction competes with homotypic interactions between the N termini of different HttEx1Qn molecules that trigger the aggregation process. Our results lay the foundations of future therapeutic strategies targeting huntingtin aggregation in Huntington disease.
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Affiliation(s)
- Elodie Monsellier
- From the Neuroscience Paris-Saclay Institute, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Virginie Redeker
- From the Neuroscience Paris-Saclay Institute, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Gemma Ruiz-Arlandis
- From the Neuroscience Paris-Saclay Institute, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Luc Bousset
- From the Neuroscience Paris-Saclay Institute, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Ronald Melki
- From the Neuroscience Paris-Saclay Institute, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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29
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Vadlamani G, Thomas MD, Patel TR, Donald LJ, Reeve TM, Stetefeld J, Standing KG, Vocadlo DJ, Mark BL. The β-lactamase gene regulator AmpR is a tetramer that recognizes and binds the D-Ala-D-Ala motif of its repressor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. J Biol Chem 2014; 290:2630-43. [PMID: 25480792 DOI: 10.1074/jbc.m114.618199] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inducible expression of chromosomal AmpC β-lactamase is a major cause of β-lactam antibiotic resistance in the Gram-negative bacteria Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is induced by the LysR-type transcriptional regulator (LTTR) AmpR, which activates ampC expression in response to changes in peptidoglycan (PG) metabolite levels that occur during exposure to β-lactams. Under normal conditions, AmpR represses ampC transcription by binding the PG precursor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. When exposed to β-lactams, however, PG catabolites (1,6-anhydroMurNAc-peptides) accumulate in the cytosol, which have been proposed to competitively displace UDP-MurNAc-pentapeptide from AmpR and convert it into an activator of ampC transcription. Here we describe the molecular interactions between AmpR (from Citrobacter freundii), its DNA operator, and repressor UDP-MurNAc-pentapeptide. Non-denaturing mass spectrometry revealed AmpR to be a homotetramer that is stabilized by DNA containing the T-N11-A LTTR binding motif and revealed that it can bind four repressor molecules in an apparently stepwise manner. A crystal structure of the AmpR effector-binding domain bound to UDP-MurNAc-pentapeptide revealed that the terminal D-Ala-D-Ala motif of the repressor forms the primary contacts with the protein. This observation suggests that 1,6-anhydroMurNAc-pentapeptide may convert AmpR into an activator of ampC transcription more effectively than 1,6-anhydroMurNAc-tripeptide (which lacks the D-Ala-D-Ala motif). Finally, small angle x-ray scattering demonstrates that the AmpR·DNA complex adopts a flat conformation similar to the LTTR protein AphB and undergoes only a slight conformational change when binding UDP-MurNAc-pentapeptide. Modeling the AmpR·DNA tetramer bound to UDP-MurNAc-pentapeptide predicts that the UDP-MurNAc moiety of the repressor participates in modulating AmpR function.
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Affiliation(s)
| | | | | | | | | | | | - Kenneth G Standing
- Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - David J Vocadlo
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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30
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Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem 2014; 290:3308-32. [PMID: 25451919 DOI: 10.1074/jbc.m114.611525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 01/01/2023] Open
Abstract
CYP3A4 is an abundant and catalytically dominant human liver endoplasmic reticulum-anchored cytochrome P450 enzyme engaged in the biotransformation of endo- and xenobiotics, including >50% of clinically relevant drugs. Alterations of CYP3A4 protein turnover can influence clinically relevant drug metabolism and bioavailability and drug-drug interactions. This CYP3A4 turnover involves endoplasmic reticulum-associated degradation via the ubiquitin (Ub)-dependent 26 S proteasomal system that relies on two highly complementary E2 Ub-conjugating-E3 Ub-ligase (UBC7-gp78 and UbcH5a-C terminus of Hsc70-interacting protein (CHIP)-Hsc70-Hsp40) complexes, as well as protein kinases (PK) A and C. We have documented that CYP3A4 Ser/Thr phosphorylation (Ser(P)/Thr(P)) by PKA and/or PKC accelerates/enhances its Lys ubiquitination by either of these E2-E3 systems. Intriguingly, CYP3A4 Ser(P)/Thr(P) and ubiquitinated Lys residues reside within the cytosol-accessible surface loop and/or conformationally assembled acidic Asp/Glu clusters, leading us to propose that such post-translational Ser/Thr protein phosphorylation primes CYP3A4 for ubiquitination. Herein, this possibility was examined through various complementary approaches, including site-directed mutagenesis, chemical cross-linking, peptide mapping, and LC-MS/MS analyses. Our findings reveal that such CYP3A4 Asp/Glu/Ser(P)/Thr(P) surface clusters are indeed important for its intermolecular electrostatic interactions with each of these E2-E3 subcomponents. By imparting additional negative charge to these Asp/Glu clusters, such Ser/Thr phosphorylation would generate P450 phosphodegrons for molecular recognition by the E2-E3 complexes, thereby controlling the timing of CYP3A4 ubiquitination and endoplasmic reticulum-associated degradation. Although the importance of phosphodegrons in the CHIP targeting of its substrates is known, to our knowledge this is the first example of phosphodegron involvement in gp78-substrate recruitment, an important step in CYP3A4 proteasomal degradation.
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Affiliation(s)
- YongQiang Wang
- From the Departments of Cellular and Molecular Pharmacology
| | - Sung-Mi Kim
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Yi Liu
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Maria Almira Correia
- From the Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco, San Francisco, California 94158-2517
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31
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Fedosejevs ET, Ying S, Park J, Anderson EM, Mullen RT, She YM, Plaxton WC. Biochemical and molecular characterization of RcSUS1, a cytosolic sucrose synthase phosphorylated in vivo at serine 11 in developing castor oil seeds. J Biol Chem 2014; 289:33412-24. [PMID: 25313400 PMCID: PMC4246097 DOI: 10.1074/jbc.m114.585554] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 10/06/2014] [Indexed: 11/06/2022] Open
Abstract
Sucrose synthase (SUS) catalyzes the UDP-dependent cleavage of sucrose into UDP-glucose and fructose and has become an important target for improving seed crops via metabolic engineering. A UDP-specific SUS homotetramer composed of 93-kDa subunits was purified to homogeneity from the triacylglyceride-rich endosperm of developing castor oil seeds (COS) and identified as RcSUS1 by mass spectrometry. RcSUS1 transcripts peaked during early development, whereas levels of SUS activity and immunoreactive 93-kDa SUS polypeptides maximized during mid-development, becoming undetectable in fully mature COS. The cytosolic location of the enzyme was established following transient expression of RcSUS1-enhanced YFP in tobacco suspension cells and fluorescence microscopy. Immunological studies using anti-phosphosite-specific antibodies revealed dynamic and high stoichiometric in vivo phosphorylation of RcSUS1 at its conserved Ser-11 residue during COS development. Incorporation of (32)P(i) from [γ-(32)P]ATP into a RcSUS1 peptide substrate, alongside a phosphosite-specific ELISA assay, established the presence of calcium-dependent RcSUS1 (Ser-11) kinase activity. Approximately 10% of RcSUS1 was associated with COS microsomal membranes and was hypophosphorylated relative to the remainder of RcSUS1 that partitioned into the soluble, cytosolic fraction. Elimination of sucrose supply caused by excision of intact pods of developing COS abolished RcSUS1 transcription while triggering the progressive dephosphorylation of RcSUS1 in planta. This did not influence the proportion of RcSUS1 associated with microsomal membranes but instead correlated with a subsequent marked decline in SUS activity and immunoreactive RcSUS1 polypeptides. Phosphorylation at Ser-11 appears to protect RcSUS1 from proteolysis, rather than influence its kinetic properties or partitioning between the soluble cytosol and microsomal membranes.
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Affiliation(s)
| | | | - Joonho Park
- the Department of Fine Chemistry, Seoul National University of Science and Technology, Nowon-Gu, Seoul 139-743, Korea
| | - Erin M Anderson
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada, and
| | - Robert T Mullen
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada, and
| | - Yi-Min She
- the Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China
| | - William C Plaxton
- From the Departments of Biology and Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada,
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32
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Abstract
Exosomes are small vesicles released from cells into extracellular space. We have isolated exosomes from neuroblastoma cells and investigated their influence on the aggregation of α-synuclein, a protein associated with Parkinson disease pathology. Using cryo-transmission electron microscopy of exosomes, we found spherical unilamellar vesicles with a significant protein content, and Western blot analysis revealed that they contain, as expected, the proteins Flotillin-1 and Alix. Using thioflavin T fluorescence to monitor aggregation kinetics, we found that exosomes catalyze the process in a similar manner as a low concentration of preformed α-synuclein fibrils. The exosomes reduce the lag time indicating that they provide catalytic environments for nucleation. The catalytic effects of exosomes derived from naive cells and cells that overexpress α-synuclein do not differ. Vesicles prepared from extracted exosome lipids accelerate aggregation, suggesting that the lipids in exosomes are sufficient for the catalytic effect to arise. Using mass spectrometry, we found several phospholipid classes in the exosomes, including phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, phosphatidylinositol, and the gangliosides GM2 and GM3. Within each class, several species with different acyl chains were identified. We then prepared vesicles from corresponding pure lipids or defined mixtures, most of which were found to retard α-synuclein aggregation. As a striking exception, vesicles containing ganglioside lipids GM1 or GM3 accelerate the process. Understanding how α-synuclein interacts with biological membranes to promote neurological disease might lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Marie Grey
- From the Departments of Physical Chemistry
| | - Christopher J Dunning
- the Neuronal Survival Unit, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, SE-22100 Lund, Sweden and the Center for Neurodegenerative Science, Biochemistry and Structural Biology, and
| | - Ricardo Gaspar
- From the Departments of Physical Chemistry, Biochemistry and Structural Biology, and
| | | | - Patrik Brundin
- the Neuronal Survival Unit, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, SE-22100 Lund, Sweden and the Center for Neurodegenerative Science, The Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Emma Sparr
- From the Departments of Physical Chemistry,
| | - Sara Linse
- Biochemistry and Structural Biology, and
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33
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Wickramaratne S, Boldry EJ, Buehler C, Wang YC, Distefano MD, Tretyakova NY. Error-prone translesion synthesis past DNA-peptide cross-links conjugated to the major groove of DNA via C5 of thymidine. J Biol Chem 2014; 290:775-87. [PMID: 25391658 DOI: 10.1074/jbc.m114.613638] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 12/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are exceptionally bulky, structurally diverse DNA adducts formed in cells upon exposure to endogenous and exogenous bis-electrophiles, reactive oxygen species, and ionizing radiation. If not repaired, DPCs can induce toxicity and mutations. It has been proposed that the protein component of a DPC is proteolytically degraded, giving rise to smaller DNA-peptide conjugates, which can be subject to nucleotide excision repair and replication bypass. In this study, polymerase bypass of model DNA-peptide conjugates structurally analogous to the lesions induced by reactive oxygen species and DNA methyltransferase inhibitors was examined. DNA oligomers containing site-specific DNA-peptide conjugates were generated by copper-catalyzed [3 + 2] Huisgen cyclo-addition between an alkyne-functionalized C5-thymidine in DNA and an azide-containing 10-mer peptide. The resulting DNA-peptide conjugates were subjected to steady-state kinetic experiments in the presence of recombinant human lesion bypass polymerases κ and η, followed by PAGE-based assays to determine the catalytic efficiency and the misinsertion frequency opposite the lesion. We found that human polymerase κ and η can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, whereas human polymerase η preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI(-)-MS/MS sequencing of the extension products has revealed that post-lesion synthesis was highly error-prone, resulting in mutations opposite the adducted site or at the +1 position from the adduct and multiple deletions. Collectively, our results indicate that replication bypass of peptides conjugated to the C5 position of thymine by human translesion synthesis polymerases leads to large numbers of base substitution and frameshift mutations.
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Affiliation(s)
- Susith Wickramaratne
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily J Boldry
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and
| | - Charles Buehler
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Yen-Chih Wang
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark D Distefano
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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Brett K, Kordyukova LV, Serebryakova MV, Mintaev RR, Alexeevski AV, Veit M. Site-specific S-acylation of influenza virus hemagglutinin: the location of the acylation site relative to the membrane border is the decisive factor for attachment of stearate. J Biol Chem 2014; 289:34978-89. [PMID: 25349209 DOI: 10.1074/jbc.m114.586180] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 12/21/2022] Open
Abstract
S-Acylation of hemagglutinin (HA), the main glycoprotein of influenza viruses, is an essential modification required for virus replication. Using mass spectrometry, we have previously demonstrated specific attachment of acyl chains to individual acylation sites. Whereas the two cysteines in the cytoplasmic tail of HA contain only palmitate, stearate is exclusively attached to a cysteine positioned at the end of the transmembrane region (TMR). Here we analyzed recombinant viruses containing HA with exchange of conserved amino acids adjacent to acylation sites or with a TMR cysteine shifted to a cytoplasmic location to identify the molecular signal that determines preferential attachment of stearate. We first developed a new protocol for sample preparation that requires less material and might thus also be suitable to analyze cellular proteins. We observed cell type-specific differences in the fatty acid pattern of HA: more stearate was attached if human viruses were grown in mammalian compared with avian cells. No underacylated peptides were detected in the mass spectra, and even mutations that prevented generation of infectious virus particles did not abolish acylation of expressed HA as demonstrated by metabolic labeling experiments with [(3)H]palmitate. Exchange of conserved amino acids in the vicinity of an acylation site had a moderate effect on the stearate content. In contrast, shifting the TMR cysteine to a cytoplasmic location virtually eliminated attachment of stearate. Thus, the location of an acylation site relative to the transmembrane span is the main signal for stearate attachment, but the sequence context and the cell type modulate the fatty acid pattern.
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Affiliation(s)
- Katharina Brett
- From the Institut für Virologie, Free University Berlin, 14163 Berlin, Germany
| | - Larisa V Kordyukova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina V Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ramil R Mintaev
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, I. I. Mechnikov Research Institute of Vaccines and Sera, Russian Academy of Medical Sciences, 105064 Moscow, Russia, and
| | - Andrei V Alexeevski
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Michael Veit
- From the Institut für Virologie, Free University Berlin, 14163 Berlin, Germany,
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35
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McCorvie TJ, Kopec J, Hyung SJ, Fitzpatrick F, Feng X, Termine D, Strain-Damerell C, Vollmar M, Fleming J, Janz JM, Bulawa C, Yue WW. Inter-domain communication of human cystathionine β-synthase: structural basis of S-adenosyl-L-methionine activation. J Biol Chem 2014; 289:36018-30. [PMID: 25336647 PMCID: PMC4276868 DOI: 10.1074/jbc.m114.610782] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cystathionine β-synthase (CBS) is a key enzyme in sulfur metabolism, and its inherited deficiency causes homocystinuria. Mammalian CBS is modulated by the binding of S-adenosyl-l-methionine (AdoMet) to its regulatory domain, which activates its catalytic domain. To investigate the underlying mechanism, we performed x-ray crystallography, mutagenesis, and mass spectrometry (MS) on human CBS. The 1.7 Å structure of a AdoMet-bound CBS regulatory domain shows one AdoMet molecule per monomer, at the interface between two constituent modules (CBS-1, CBS-2). AdoMet binding is accompanied by a reorientation between the two modules, relative to the AdoMet-free basal state, to form interactions with AdoMet via residues verified by mutagenesis to be important for AdoMet binding (Phe443, Asp444, Gln445, and Asp538) and for AdoMet-driven inter-domain communication (Phe443, Asp538). The observed structural change is further supported by ion mobility MS, showing that as-purified CBS exists in two conformational populations, which converged to one in the presence of AdoMet. We therefore propose that AdoMet-induced conformational change alters the interface and arrangement between the catalytic and regulatory domains within the CBS oligomer, thereby increasing the accessibility of the enzyme active site for catalysis.
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Affiliation(s)
- Thomas J McCorvie
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jolanta Kopec
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Suk-Joon Hyung
- Worldwide Research and Development, Pfizer Inc., Groton, Connecticut 06340, and
| | - Fiona Fitzpatrick
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Xidong Feng
- Worldwide Research and Development, Pfizer Inc., Groton, Connecticut 06340, and
| | - Daniel Termine
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Claire Strain-Damerell
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Melanie Vollmar
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - James Fleming
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Jay M Janz
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Christine Bulawa
- the Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts 02140
| | - Wyatt W Yue
- From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom,
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36
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Gray EJ, Petsalaki E, James DA, Bagshaw RD, Stacey MM, Rocks O, Gingras AC, Pawson T. Src homology 2 domain containing protein 5 (SH2D5) binds the breakpoint cluster region protein, BCR, and regulates levels of Rac1-GTP. J Biol Chem 2014; 289:35397-408. [PMID: 25331951 DOI: 10.1074/jbc.m114.615112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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
SH2D5 is a mammalian-specific, uncharacterized adaptor-like protein that contains an N-terminal phosphotyrosine-binding domain and a C-terminal Src homology 2 (SH2) domain. We show that SH2D5 is highly enriched in adult mouse brain, particularly in Purkinjie cells in the cerebellum and the cornu ammonis of the hippocampus. Despite harboring two potential phosphotyrosine (Tyr(P)) recognition domains, SH2D5 binds minimally to Tyr(P) ligands, consistent with the absence of a conserved Tyr(P)-binding arginine residue in the SH2 domain. Immunoprecipitation coupled to mass spectrometry (IP-MS) from cultured cells revealed a prominent association of SH2D5 with breakpoint cluster region protein, a RacGAP that is also highly expressed in brain. This interaction occurred between the phosphotyrosine-binding domain of SH2D5 and an NxxF motif located within the N-terminal region of the breakpoint cluster region. siRNA-mediated depletion of SH2D5 in a neuroblastoma cell line, B35, induced a cell rounding phenotype correlated with low levels of activated Rac1-GTP, suggesting that SH2D5 affects Rac1-GTP levels. Taken together, our data provide the first characterization of the SH2D5 signaling protein.
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Affiliation(s)
- Elizabeth J Gray
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Evangelia Petsalaki
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - D Andrew James
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, Sanofi Pasteur, Toronto, Ontario M2R3T4, Canada, and
| | - Richard D Bagshaw
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Melissa M Stacey
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Oliver Rocks
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, the Max Delbrück Center for Molecular Medicine Berlin-Buch, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Anne-Claude Gingras
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Tony Pawson
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
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37
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Bray L, Froment C, Pardo P, Candotto C, Burlet-Schiltz O, Zajac JM, Mollereau C, Moulédous L. Identification and functional characterization of the phosphorylation sites of the neuropeptide FF2 receptor. J Biol Chem 2014; 289:33754-66. [PMID: 25326382 DOI: 10.1074/jbc.m114.612614] [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
The neuropeptide FF2 (NPFF2) receptor belongs to the rhodopsin family of G protein-coupled receptors and mediates the effects of several related RFamide neuropeptides. One of the main pharmacological interests of this system resides in its ability to regulate endogenous opioid systems, making it a potential target to reduce the negative effects of chronic opioid use. Phosphorylation of intracellular residues is the most extensively studied post-translational modification regulating G protein-coupled receptor activity. However, until now, no information concerning NPFF2 receptor phosphorylation is available. In this study, we combined mass spectrometric analysis and site-directed mutagenesis to analyze for the first time the phosphorylation pattern of the NPFF2 receptor and the role of the various phosphorylation sites in receptor signaling, desensitization, and trafficking in a SH-SY5Y model cell line. We identified the major, likely GRK-dependent, phosphorylation cluster responsible for acute desensitization, (412)TNST(415) at the end of the C terminus of the receptor, and additional sites involved in desensitization ((372)TS(373)) and internalization (Ser(395)). We thus demonstrate the key role played by phosphorylation in the regulation of NPFF2 receptor activity and trafficking. Our data also provide additional evidence supporting the concept that desensitization and internalization are partially independent processes relying on distinct phosphorylation patterns.
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Affiliation(s)
- Lauriane Bray
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Carine Froment
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Pardo
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Cédric Candotto
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Jean-Marie Zajac
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Catherine Mollereau
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Lionel Moulédous
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
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38
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Peng HM, Liu J, Forsberg SE, Tran HT, Anderson SM, Auchus RJ. Catalytically relevant electrostatic interactions of cytochrome P450c17 (CYP17A1) and cytochrome b5. J Biol Chem 2014; 289:33838-49. [PMID: 25315771 DOI: 10.1074/jbc.m114.608919] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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
Two acidic residues, Glu-48 and Glu-49, of cytochrome b5 (b5) are essential for stimulating the 17,20-lyase activity of cytochrome P450c17 (CYP17A1). Substitution of Ala, Gly, Cys, or Gln for these two glutamic acid residues abrogated all capacity to stimulate 17,20-lyase activity. Mutations E49D and E48D/E49D retained 23 and 38% of wild-type activity, respectively. Using the zero-length cross-linker ethyl-3-(3-dimethylaminopropyl)carbodiimide, we obtained cross-linked heterodimers of b5 and CYP17A1, wild-type, or mutations R347K and R358K. In sharp contrast, the b5 double mutation E48G/E49G did not form cross-linked complexes with wild-type CYP17A1. Mass spectrometric analysis of the CYP17A1-b5 complexes identified two cross-linked peptide pairs as follows: CYP17A1-WT: (84)EVLIKK(89)-b5: (53)EQAGGDATENFEDVGHSTDAR(73) and CYP17A1-R347K: (341)TPTISDKNR(349)-b5: (40)FLEEHPGGEEVLR(52). Using these two sites of interaction and Glu-48/Glu-49 in b5 as constraints, protein docking calculations based on the crystal structures of the two proteins yielded a structural model of the CYP17A1-b5 complex. The appositional surfaces include Lys-88, Arg-347, and Arg-358/Arg-449 of CYP17A1, which interact with Glu-61, Glu-42, and Glu-48/Glu-49 of b5, respectively. Our data reveal the structural basis of the electrostatic interactions between these two proteins, which is critical for 17,20-lyase activity and androgen biosynthesis.
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Affiliation(s)
- Hwei-Ming Peng
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Jiayan Liu
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Sarah E Forsberg
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | | | - Sean M Anderson
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Richard J Auchus
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
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39
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Montigny C, Decottignies P, Le Maréchal P, Capy P, Bublitz M, Olesen C, Møller JV, Nissen P, le Maire M. S-palmitoylation and s-oleoylation of rabbit and pig sarcolipin. J Biol Chem 2014; 289:33850-61. [PMID: 25301946 DOI: 10.1074/jbc.m114.590307] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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
Sarcolipin (SLN) is a regulatory peptide present in sarcoplasmic reticulum (SR) from skeletal muscle of animals. We find that native rabbit SLN is modified by a fatty acid anchor on Cys-9 with a palmitic acid in about 60% and, surprisingly, an oleic acid in the remaining 40%. SLN used for co-crystallization with SERCA1a (Winther, A. M., Bublitz, M., Karlsen, J. L., Moller, J. V., Hansen, J. B., Nissen, P., and Buch-Pedersen, M. J. (2013) Nature 495, 265-2691; Ref. 1) is also palmitoylated/oleoylated, but is not visible in crystal structures, probably due to disorder. Treatment with 1 m hydroxylamine for 1 h removes the fatty acids from a majority of the SLN pool. This treatment did not modify the SERCA1a affinity for Ca(2+) but increased the Ca(2+)-dependent ATPase activity of SR membranes indicating that the S-acylation of SLN or of other proteins is required for this effect on SERCA1a. Pig SLN is also fully palmitoylated/oleoylated on its Cys-9 residue, but in a reverse ratio of about 40/60. An alignment of 67 SLN sequences from the protein databases shows that 19 of them contain a cysteine and the rest a phenylalanine at position 9. Based on a cladogram, we postulate that the mutation from phenylalanine to cysteine in some species is the result of an evolutionary convergence. We suggest that, besides phosphorylation, S-acylation/deacylation also regulates SLN activity.
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Affiliation(s)
- Cédric Montigny
- From the Laboratoire des Protéines Membranaires, UMR 8221, Commissariat à l'Energie Atomique (CEA), Université Paris-Sud and Centre National de la Recherche Scientifique (CNRS), F91191, Gif-sur-Yvette, France
| | - Paulette Decottignies
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS UMR 8619, Université Paris-Sud, F91400, Orsay, France
| | - Pierre Le Maréchal
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS UMR 8619, Université Paris-Sud, F91400, Orsay, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes et Spéciation, CNRS UPR 9034, Centre de Recherche de Gif and Université Paris-Sud, F91190, Gif-sur-Yvette, France
| | - Maike Bublitz
- Centre for Membrane Pumps in Cells and Disease, PUMPKIN, Danish National Research Foundation, Department of Molecular Biology and Genetics, and
| | - Claus Olesen
- Centre for Membrane Pumps in Cells and Disease, PUMPKIN, Danish National Research Foundation, Department of Molecular Biology and Genetics, and Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
| | - Jesper Vuust Møller
- Centre for Membrane Pumps in Cells and Disease, PUMPKIN, Danish National Research Foundation, Department of Molecular Biology and Genetics, and
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease, PUMPKIN, Danish National Research Foundation, Department of Molecular Biology and Genetics, and
| | - Marc le Maire
- From the Laboratoire des Protéines Membranaires, UMR 8221, Commissariat à l'Energie Atomique (CEA), Université Paris-Sud and Centre National de la Recherche Scientifique (CNRS), F91191, Gif-sur-Yvette, France,
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40
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Tal O, Trabelcy B, Gerchman Y, Adir N. Investigation of phycobilisome subunit interaction interfaces by coupled cross-linking and mass spectrometry. J Biol Chem 2014; 289:33084-97. [PMID: 25296757 DOI: 10.1074/jbc.m114.595942] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phycobilisome (PBS) is an extremely large light-harvesting complex, common in cyanobacteria and red algae, composed of rods and core substructures. These substructures are assembled from chromophore-bearing phycocyanin and allophycocyanin subunits, nonpigmented linker proteins and in some cases additional subunits. To date, despite the determination of crystal structures of isolated PBS components, critical questions regarding the interaction and energy flow between rods and core are still unresolved. Additionally, the arrangement of minor PBS components located inside the core cylinders is unknown. Different models of the general architecture of the PBS have been proposed, based on low resolution images from electron microscopy or high resolution crystal structures of isolated components. This work presents a model of the assembly of the rods onto the core arrangement and for the positions of inner core components, based on cross-linking and mass spectrometry analysis of isolated, functional intact Thermosynechococcus vulcanus PBS, as well as functional cross-linked adducts. The experimental results were utilized to predict potential docking interactions of different protein pairs. Combining modeling and cross-linking results, we identify specific interactions within the PBS subcomponents that enable us to suggest possible functional interactions between the chromophores of the rods and the core and improve our understanding of the assembly, structure, and function of PBS.
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Affiliation(s)
- Ofir Tal
- From the Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel and
| | - Beny Trabelcy
- the Department of Biology, Faculty of Natural Sciences, University of Haifa at Oranim, 36006 Tivon, Israel
| | - Yoram Gerchman
- the Department of Biology, Faculty of Natural Sciences, University of Haifa at Oranim, 36006 Tivon, Israel
| | - Noam Adir
- From the Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel and
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41
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Resetca D, Haftchenary S, Gunning PT, Wilson DJ. Changes in signal transducer and activator of transcription 3 (STAT3) dynamics induced by complexation with pharmacological inhibitors of Src homology 2 (SH2) domain dimerization. J Biol Chem 2014; 289:32538-47. [PMID: 25288792 DOI: 10.1074/jbc.m114.595454] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 12/29/2022] Open
Abstract
The activity of the transcription factor signal transducer and activator of transcription 3 (STAT3) is dysregulated in a number of hematological and solid malignancies. Development of pharmacological STAT3 Src homology 2 (SH2) domain interaction inhibitors holds great promise for cancer therapy, and a novel class of salicylic acid-based STAT3 dimerization inhibitors that includes orally bioavailable drug candidates has been recently developed. The compounds SF-1-066 and BP-1-102 are predicted to bind to the STAT3 SH2 domain. However, given the highly unstructured and dynamic nature of the SH2 domain, experimental confirmation of this prediction was elusive. We have interrogated the protein-ligand interaction of STAT3 with these small molecule inhibitors by means of time-resolved electrospray ionization hydrogen-deuterium exchange mass spectrometry. Analysis of site-specific evolution of deuterium uptake induced by the complexation of STAT3 with SF-1-066 or BP-1-102 under physiological conditions enabled the mapping of the in silico predicted inhibitor binding site to the STAT3 SH2 domain. The binding of both inhibitors to the SH2 domain resulted in significant local decreases in dynamics, consistent with solvent exclusion at the inhibitor binding site and increased rigidity of the inhibitor-complexed SH2 domain. Interestingly, inhibitor binding induced hot spots of allosteric perturbations outside of the SH2 domain, manifesting mainly as increased deuterium uptake, in regions of STAT3 important for DNA binding and nuclear localization.
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Affiliation(s)
- Diana Resetca
- From the Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada and
| | - Sina Haftchenary
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Derek J Wilson
- From the Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada and
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42
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Eriksson O, Ramström M, Hörnaeus K, Bergquist J, Mokhtari D, Siegbahn A. The Eph tyrosine kinase receptors EphB2 and EphA2 are novel proteolytic substrates of tissue factor/coagulation factor VIIa. J Biol Chem 2014; 289:32379-91. [PMID: 25281742 DOI: 10.1074/jbc.m114.599332] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 01/31/2023] Open
Abstract
Tissue factor (TF) binds the serine protease factor VIIa (FVIIa) to form a proteolytically active complex that can trigger coagulation or activate cell signaling. Here we addressed the involvement of tyrosine kinase receptors (RTKs) in TF/FVIIa signaling by antibody array analysis and subsequently found that EphB2 and EphA2 of the Eph RTK family were cleaved in their ectodomains by TF/FVIIa. We used N-terminal Edman sequencing and LC-MS/MS analysis to characterize the cleaved Eph isoforms and identified a key arginine residue at the cleavage site, in agreement with the tryptic serine protease activity of FVIIa. Protease-activated receptor 2 (PAR2) signaling and downstream coagulation activity was non-essential in this context, in further support of a direct cleavage by TF/FVIIa. EphB2 was cleaved by FVIIa concentrations in the subnanomolar range in a number of TF expressing cell types, indicating that the active cellular pool of TF was involved. FVIIa caused potentiation of cell repulsion by the EphB2 ligand ephrin-B1, demonstrating a novel proteolytical event to control Eph-mediated cell segregation. These results define Eph RTKs as novel proteolytical targets of TF/FVIIa and provide new insights into how TF/FVIIa regulates cellular functions independently of PAR2.
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Affiliation(s)
- Oskar Eriksson
- From the Department of Medical Sciences, Clinical Chemistry, Uppsala University Hospital, SE-751 85 Uppsala, Science for Life Laboratory, Uppsala University, Sweden
| | - Margareta Ramström
- the Department of Chemistry, Analytical Chemistry, BMC, SE-751 24 Uppsala, and Science for Life Laboratory, Uppsala University, Sweden
| | - Katarina Hörnaeus
- the Department of Chemistry, Analytical Chemistry, BMC, SE-751 24 Uppsala, and Science for Life Laboratory, Uppsala University, Sweden
| | - Jonas Bergquist
- the Department of Chemistry, Analytical Chemistry, BMC, SE-751 24 Uppsala, and Science for Life Laboratory, Uppsala University, Sweden
| | - Dariush Mokhtari
- From the Department of Medical Sciences, Clinical Chemistry, Uppsala University Hospital, SE-751 85 Uppsala, Science for Life Laboratory, Uppsala University, Sweden
| | - Agneta Siegbahn
- From the Department of Medical Sciences, Clinical Chemistry, Uppsala University Hospital, SE-751 85 Uppsala, Science for Life Laboratory, Uppsala University, Sweden
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Jin Z, Berthiaume JM, Li Q, Henry F, Huang Z, Sadhukhan S, Gao P, Tochtrop GP, Puchowicz MA, Zhang GF. Catabolism of (2E)-4-hydroxy-2-nonenal via ω- and ω-1-oxidation stimulated by ketogenic diet. J Biol Chem 2014; 289:32327-32338. [PMID: 25274632 DOI: 10.1074/jbc.m114.602458] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress triggers the peroxidation of ω-6-polyunsaturated fatty acids to reactive lipid fragments, including (2E)-4-hydroxy-2-nonenal (HNE). We previously reported two parallel catabolic pathways of HNE. In this study, we report a novel metabolite that accumulates in rat liver perfused with HNE or 4-hydroxynonanoic acid (HNA), identified as 3-(5-oxotetrahydro-2-furanyl)propanoyl-CoA. In experiments using a combination of isotopic analysis and metabolomics studies, three catabolic pathways of HNE were delineated following HNE conversion to HNA. (i) HNA is ω-hydroxylated to 4,9-dihydroxynonanoic acid, which is subsequently oxidized to 4-hydroxynonanedioic acid. This is followed by the degradation of 4-hydroxynonanedioic acid via β-oxidation originating from C-9 of HNA breaking down to 4-hydroxynonanedioyl-CoA, 4-hydroxyheptanedioyl-CoA, or its lactone, 2-hydroxyglutaryl-CoA, and 2-ketoglutaric acid entering the citric acid cycle. (ii) ω-1-hydroxylation of HNA leads to 4,8-dihydroxynonanoic acid (4,8-DHNA), which is subsequently catabolized via two parallel pathways we previously reported. In catabolic pathway A, 4,8-DHNA is catabolized to 4-phospho-8-hydroxynonanoyl-CoA, 3,8-dihydroxynonanoyl-CoA, 6-hydroxyheptanoyl-CoA, 4-hydroxypentanoyl-CoA, propionyl-CoA, and acetyl-CoA. (iii) The catabolic pathway B of 4,8-DHNA leads to 2,6-dihydroxyheptanoyl-CoA, 5-hydroxyhexanoyl-CoA, 3-hydroxybutyryl-CoA, and acetyl-CoA. Both in vivo and in vitro experiments showed that HNE can be catabolically disposed via ω- and ω-1-oxidation in rat liver and kidney, with little activity in brain and heart. Dietary experiments showed that ω- and ω-1-hydroxylation of HNA in rat liver were dramatically up-regulated by a ketogenic diet, which lowered HNE basal level. HET0016 inhibition and mRNA expression level suggested that the cytochrome P450 4A are main enzymes responsible for the NADPH-dependent ω- and ω-1-hydroxylation of HNA/HNE.
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Affiliation(s)
- Zhicheng Jin
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jessica M Berthiaume
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106; Departments of Physiology and Biophysics, and Case Western Reserve University, Cleveland, Ohio 44106
| | - Qingling Li
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Fabrice Henry
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Zhong Huang
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Sushabhan Sadhukhan
- Departments of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Peng Gao
- Departments of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Gregory P Tochtrop
- Departments of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Michelle A Puchowicz
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Guo-Fang Zhang
- Departments of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106.
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Kaur D, Angala SK, Wu SW, Khoo KH, Chatterjee D, Brennan PJ, Jackson M, McNeil MR. A single arabinan chain is attached to the phosphatidylinositol mannosyl core of the major immunomodulatory mycobacterial cell envelope glycoconjugate, lipoarabinomannan. J Biol Chem 2014; 289:30249-30256. [PMID: 25231986 DOI: 10.1074/jbc.m114.599415] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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
Lipoarabinomannan (LAM) is composed of a phosphatidylinositol anchor followed by a mannan followed by an arabinan that may be capped with various motifs including oligosaccharides of mannose. A related polymer, lipomannan (LM), is composed of only the phosphatidylinositol and mannan core. Both the structure and the biosynthesis of LAM have been studied extensively. However, fundamental questions about the branching structure of LM and the number of arabinan chains on the mannan backbone in LAM remain. LM and LAM molecules produced by three different glycosyltransferase mutants of Mycobacterium smegmatis were used here to investigate these questions. Using an MSMEG_4241 mutant that lacks the α-(1,6)-mannosyltransferase used late in LM elongation, we showed that the reducing end region of the mannan that is attached to inositol has 5-7 unbranched α-6-linked-mannosyl residues followed by two or three α-6-linked mannosyl residues branched with single α-mannopyranose residues at O-2. After these branched mannosyl residues, the α-6-linked mannan chain is terminated with an α-mannopyranose at O-2 rather than O-6 of the penultimate residue. Analysis of the number of arabinans attached to the mannan core of LM in two other mutants (ΔembC and ΔMSMEG_4247) demonstrated exactly one arabinosyl substitution of the mannan core suggestive of the arabinosylation of a linear LM precursor with ∼10-12 mannosyl residues followed by additional mannosylation of the core and arabinosylation of a single arabinosyl "primer." Thus, these studies suggest that only a single arabinan chain attached near the middle of the mannan core is present in mature LAM and allow for an updated working model of the biosynthetic pathway of LAM and LM.
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Affiliation(s)
- Devinder Kaur
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and
| | - Sz-Wei Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and
| | - Patrick J Brennan
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and.
| | - Michael R McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523 and.
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45
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Pinto JT, Krasnikov BF, Alcutt S, Jones ME, Dorai T, Villar MT, Artigues A, Li J, Cooper AJL. Kynurenine aminotransferase III and glutamine transaminase L are identical enzymes that have cysteine S-conjugate β-lyase activity and can transaminate L-selenomethionine. J Biol Chem 2014; 289:30950-61. [PMID: 25231977 DOI: 10.1074/jbc.m114.591461] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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
Three of the four kynurenine aminotransferases (KAT I, II, and IV) that synthesize kynurenic acid, a neuromodulator, are identical to glutamine transaminase K (GTK), α-aminoadipate aminotransferase, and mitochondrial aspartate aminotransferase, respectively. GTK/KAT I and aspartate aminotransferase/KAT IV possess cysteine S-conjugate β-lyase activity. The gene for the former enzyme, GTK/KAT I, is listed in mammalian genome data banks as CCBL1 (cysteine conjugate beta-lyase 1). Also listed, despite the fact that no β-lyase activity has been assigned to the encoded protein in the genome data bank, is a CCBL2 (synonym KAT III). We show that human KAT III/CCBL2 possesses cysteine S-conjugate β-lyase activity, as does mouse KAT II. Thus, depending on the nature of the substrate, all four KATs possess cysteine S-conjugate β-lyase activity. These present studies show that KAT III and glutamine transaminase L are identical enzymes. This report also shows that KAT I, II, and III differ in their ability to transaminate methyl-L-selenocysteine (MSC) and L-selenomethionine (SM) to β-methylselenopyruvate (MSP) and α-ketomethylselenobutyrate, respectively. Previous studies have identified these seleno-α-keto acids as potent histone deacetylase inhibitors. Methylselenol (CH3SeH), also purported to have chemopreventive properties, is the γ-elimination product of SM and the β-elimination product of MSC catalyzed by cystathionine γ-lyase (γ-cystathionase). KAT I, II, and III, in part, can catalyze β-elimination reactions with MSC generating CH3SeH. Thus, the anticancer efficacy of MSC and SM will depend, in part, on the endogenous expression of various KAT enzymes and cystathionine γ-lyase present in target tissue coupled with the ability of cells to synthesize in situ either CH3SeH and/or seleno-keto acid metabolites.
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Affiliation(s)
- John T Pinto
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Steven Alcutt
- From the Departments of Biochemistry and Molecular Biology and
| | - Melanie E Jones
- From the Departments of Biochemistry and Molecular Biology and
| | - Thambi Dorai
- Urology, New York Medical College, Valhalla, New York 10595
| | - Maria T Villar
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
| | - Antonio Artigues
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
| | - Jianyong Li
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061
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46
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Nemeria NS, Ambrus A, Patel H, Gerfen G, Adam-Vizi V, Tretter L, Zhou J, Wang J, Jordan F. Human 2-oxoglutarate dehydrogenase complex E1 component forms a thiamin-derived radical by aerobic oxidation of the enamine intermediate. J Biol Chem 2014; 289:29859-73. [PMID: 25210035 DOI: 10.1074/jbc.m114.591073] [Citation(s) in RCA: 37] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Herein are reported unique properties of the human 2-oxoglutarate dehydrogenase multienzyme complex (OGDHc), a rate-limiting enzyme in the Krebs (citric acid) cycle. (a) Functionally competent 2-oxoglutarate dehydrogenase (E1o-h) and dihydrolipoyl succinyltransferase components have been expressed according to kinetic and spectroscopic evidence. (b) A stable free radical, consistent with the C2-(C2α-hydroxy)-γ-carboxypropylidene thiamin diphosphate (ThDP) cation radical was detected by electron spin resonance upon reaction of the E1o-h with 2-oxoglutarate (OG) by itself or when assembled from individual components into OGDHc. (c) An unusual stability of the E1o-h-bound C2-(2α-hydroxy)-γ-carboxypropylidene thiamin diphosphate (the "ThDP-enamine"/C2α-carbanion, the first postdecarboxylation intermediate) was observed, probably stabilized by the 5-carboxyl group of OG, not reported before. (d) The reaction of OG with the E1o-h gave rise to superoxide anion and hydrogen peroxide (reactive oxygen species (ROS)). (e) The relatively stable enzyme-bound enamine is the likely substrate for oxidation by O2, leading to the superoxide anion radical (in d) and the radical (in b). (f) The specific activity assessed for ROS formation compared with the NADH (overall complex) activity, as well as the fraction of radical intermediate occupying active centers of E1o-h are consistent with each other and indicate that radical/ROS formation is an "off-pathway" side reaction comprising less than 1% of the "on-pathway" reactivity. However, the nearly ubiquitous presence of OGDHc in human tissues, including the brain, makes these findings of considerable importance in human metabolism and perhaps disease.
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Affiliation(s)
- Natalia S Nemeria
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Attila Ambrus
- the Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest 1094, Hungary, and
| | - Hetalben Patel
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Gary Gerfen
- the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Vera Adam-Vizi
- the Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest 1094, Hungary, and
| | - Laszlo Tretter
- the Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest 1094, Hungary, and
| | - Jieyu Zhou
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Junjie Wang
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Frank Jordan
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102,
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47
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Bonar D, Hanisch FG. Trefoil factor family domains represent highly efficient conformational determinants for N-linked N,N'-di-N-acetyllactosediamine (LacdiNAc) synthesis. J Biol Chem 2014; 289:29677-90. [PMID: 25210040 DOI: 10.1074/jbc.m114.596049] [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
The disaccharide N,N'-di-N-acetyllactose diamine (LacdiNAc, GalNAcβ1-4GlcNAcβ) is found in a limited number of extracellular matrix glycoproteins and neuropeptide hormones indicating a protein-specific transfer of GalNAc by the glycosyltransferases β4GalNAc-T3/T4. Whereas previous studies have revealed evidence for peptide determinants as controlling elements in LacdiNAc biosynthesis, we report here on an entirely independent conformational control of GalNAc transfer by single TFF (Trefoil factor) domains as high stringency determinants. Human TFF2 was recombinantly expressed in HEK-293 cells as a wild type full-length probe (TFF2-Fl, containing TFF domains P1 and P2), as single P1 or P2 domain probes, as a series of Cys/Gly mutant forms with aberrant domain structures, and as a double point-mutated probe (T68Q/F59Q) lacking aromatic residues within a hydrophobic patch. The N-glycosylation probes were analyzed by mass spectrometry for their glycoprofiles. In agreement with natural gastric TFF2, the recombinant full-length and single domain probes expressed nearly exclusively fucosylated LacdiNAc on bi-antennary complex-type chains indicating that a single TFF domain was sufficient to induce transfer of this modification. Contrasting to this, the Cys/Gly mutants showed strongly reduced LacdiNAc levels and instead preponderant LacNAc expression. The probe with point mutations of two highly conserved aromatic residues in loop 3 (T68Q/F59Q) revealed that these are essential determinant components, as the probe lacked LacdiNAc expression. The structural features of the LacdiNAc-inducing determinant on human TFF2 are discussed on the basis of crystal structures of porcine TFF2, and a series of extracellular matrix-related LacdiNAc-positive glycoproteins detected as novel candidate proteins in the secretome of HEK-293 cells.
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Affiliation(s)
- David Bonar
- From the Institute of Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany and
| | - Franz-Georg Hanisch
- From the Institute of Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany and Center for Molecular Medicine Cologne, University of Cologne, Robert-Koch-Strasse 21, 50931 Köln, Germany
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48
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Teixeira PC, Ducret A, Ferber P, Gaertner H, Hartley O, Pagano S, Butterfield M, Langen H, Vuilleumier N, Cutler P. Definition of human apolipoprotein A-I epitopes recognized by autoantibodies present in patients with cardiovascular diseases. J Biol Chem 2014; 289:28249-59. [PMID: 25170076 PMCID: PMC4192480 DOI: 10.1074/jbc.m114.589002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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] [Indexed: 12/24/2022] Open
Abstract
Autoantibodies to apolipoprotein A-I (anti-apoA-I IgG) have been shown to be both markers and mediators of cardiovascular disease, promoting atherogenesis and unstable atherosclerotic plaque. Previous studies have shown that high levels of anti-apoA-I IgGs are independently associated with major adverse cardiovascular events in patients with myocardial infarction. Autoantibody responses to apoA-I can be polyclonal and it is likely that more than one epitope may exist. To identify the specific immunoreactive peptides in apoA-I, we have developed a set of methodologies and procedures to isolate, purify, and identify novel apoA-I endogenous epitopes. First, we generated high purity apoA-I from human plasma, using thiophilic interaction chromatography followed by enzymatic digestion specifically at lysine or arginine residues. Immunoreactivity to the different peptides generated was tested by ELISA using serum obtained from patients with acute myocardial infarction and high titers of autoantibodies to native apoA-I. The immunoreactive peptides were further sequenced by mass spectrometry. Our approach successfully identified two novel immunoreactive peptides, recognized by autoantibodies from patients suffering from myocardial infarction, who contain a high titer of anti-apoA-I IgG. The discovery of these epitopes may open innovative prognostic and therapeutic opportunities potentially suitable to improve current cardiovascular risk stratification.
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Affiliation(s)
- Priscila Camillo Teixeira
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel, the Department of Genetics and Laboratory Medicine, Division of Laboratory Medicine, 1205 Geneva University Hospitals, 1205 Geneva, and
| | - Axel Ducret
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel
| | - Philippe Ferber
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel
| | - Hubert Gaertner
- the Department of Immunopathology, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Oliver Hartley
- the Department of Immunopathology, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Sabrina Pagano
- the Department of Genetics and Laboratory Medicine, Division of Laboratory Medicine, 1205 Geneva University Hospitals, 1205 Geneva, and
| | - Michelle Butterfield
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel
| | - Hanno Langen
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel
| | - Nicolas Vuilleumier
- the Department of Genetics and Laboratory Medicine, Division of Laboratory Medicine, 1205 Geneva University Hospitals, 1205 Geneva, and
| | - Paul Cutler
- From the Pharma Research and Early Development, Roche Innovation Center, 4070 Basel
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49
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Abstract
Maillard α-dicarbonyl compounds are known as central intermediates in advanced glycation end product (AGE) formation. Glucose is the primary source of energy for the human body, whereas l-threo-ascorbic acid (vitamin C) is an essential nutrient, involved in a variety of enzymatic reactions. Thus, the Maillard degradation of glucose and ascorbic acid is of major importance in vivo. To understand the complex mechanistic pathways of AGE formation, it is crucial to extend the knowledge on plasma concentrations of reactive key α-dicarbonyl compounds (e.g. 1-deoxyglucosone). With the present work, we introduce a highly sensitive LC-MS/MS multimethod for human blood plasma based on derivatization with o-phenylenediamine under acidic conditions. The impact of workup and reaction conditions, particularly of pH, was thoroughly evaluated. A comprehensive validation provided the limit of detection, limit of quantitation, coefficients of variation, and recovery rates. The method includes the α-dicarbonyls 1-deoxyglucosone, 3-deoxyglucosone, glucosone, Lederer's glucosone, dehydroascorbic acid, 2,3-diketogulonic acid, 1-deoxypentosone, 3-deoxypentosone, 3,4-dideoxypentosone, pentosone, 1-deoxythreosone, 3-deoxythreosone, threosone, methylglyoxal, glyoxal; the α-keto-carboxylic acids pyruvic acid and glyoxylic acid; and the dicarboxylic acid oxalic acid. The method was then applied to the analyses of 15 healthy subjects and 24 uremic patients undergoing hemodialysis. The comparison of the results revealed a clear shift in the product spectrum. In most cases, the plasma levels of target analytes were significantly higher. Thus, this is the first time that a complete spectrum of α-dicarbonyl compounds relevant in vivo has been established. The results provide further insights into the chemistry of AGE formation and will be helpful to find specific markers to differentiate between the various precursors of glycation.
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Affiliation(s)
| | | | - Matthias Girndt
- the Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle/Saale, Germany
| | - Christof Ulrich
- the Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle/Saale, Germany
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50
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Takahashi D, Dai H, Hiromasa Y, Krishnamoorthi R, Kanost MR. Self-association of an insect β-1,3-glucan recognition protein upon binding laminarin stimulates prophenoloxidase activation as an innate immune response. J Biol Chem 2014; 289:28399-410. [PMID: 25147183 DOI: 10.1074/jbc.m114.583971] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Insect β-glucan recognition protein (βGRP), a pathogen recognition receptor for innate immune responses, detects β-1,3-glucan on fungal surfaces via its N-terminal carbohydrate-binding domain (N-βGRP) and triggers serine protease cascades for the activation of prophenoloxidase (pro-PO) or Toll pathways. Using biophysical and biochemical methods, we characterized the interaction of the N-terminal domain from Manduca sexta βGRP2 (N-βGRP2) with laminarin, a soluble form of β-1,3-glucan. We found that carbohydrate binding by N-βGRP2 induces the formation of two types of protein-carbohydrate complexes, depending on the molar ratio of carbohydrate to protein ([C]/[P]). Precipitation, analytical ultracentrifugation, and chemical cross-linking experiments have shown that an insoluble aggregate forms when the molar ratio of carbohydrate to protein is low ([C]/[P] ∼ 1). In contrast, a soluble complex, containing at least five N-βGRP2 molecules forms at a higher molar ratio of carbohydrate/protein ([C]/[P] >5). A hypothesis that this complex is assembled partly due to protein-protein interactions was supported by chemical cross-linking experiments combined with LC-MS/MS spectrometry analysis, which permitted identification of a specific intermolecular cross-link site between N-βGRP molecules in the soluble complex. The pro-PO activation in naive plasma was strongly stimulated by addition of the insoluble aggregates of N-βGRP2. The soluble complex with laminarin formed in the plasma also stimulated pro-PO activation, but at a lower level. Taken together, these results provide experimental evidence for novel mechanisms in which associations of βGRP with microbial polysaccharide promotes assembly of βGRP oligomers, which may form a platform needed to trigger the pro-PO pathway activation cascade.
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Affiliation(s)
- Daisuke Takahashi
- From the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Huaien Dai
- From the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Yasuaki Hiromasa
- From the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Ramaswamy Krishnamoorthi
- From the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Michael R Kanost
- From the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
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