1
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Koshy D, Allardyce BJ, Dumée LF, Sutti A, Rajkhowa R, Agrawal R. Silk Industry Waste Protein-Derived Sericin Hybrid Nanoflowers for Antibiotics Remediation via Circular Economy. ACS OMEGA 2024; 9:15768-15780. [PMID: 38617643 PMCID: PMC11007843 DOI: 10.1021/acsomega.3c03367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 04/16/2024]
Abstract
Hybrid protein-copper nanoflowers have emerged as promising materials with diverse applications in biocatalysis, biosensing, and bioremediation. Sericin, a waste biopolymer from the textile industry, has shown potential for fabricating such nanoflowers. However, the influence of the molecular weight of sericin on nanoflower morphology and peroxidase-like activity remains unexplored. This work focused on the self-assembly of nanoflowers using high- and low-molecular-weight (HMW and LMW) silk sericin combined with copper(II) as an inorganic moiety. The peroxidase-like activity of the resulting nanoflowers was evaluated using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and hydrogen peroxide (H2O2). The findings revealed that high-molecular-weight sericin hybrid nanoflowers (HMW-ShNFs) exhibited significantly higher peroxidase-like activity than low-molecular-weight sericin hybrid nanoflowers (LMW-ShNFs). Furthermore, HMW-ShNFs demonstrated superior reusability and storage stability, thereby enhancing their potential for practical use. This study also explored the application of HMW-ShNF for ciprofloxacin degradation to address the environmental and health hazards posed by this antibiotic in water. The results indicated that HMW-ShNFs facilitated the degradation of ciprofloxacin, achieving a maximum degradation of 33.2 ± 1% at pH 8 and 35 °C after 72 h. Overall, the enhanced peroxidase-like activity and successful application in ciprofloxacin degradation underscore the potential of HMW-ShNFs for a sustainable and ecofriendly remediation process. These findings open avenues for the further exploration and utilization of hybrid nanoflowers in various environmental applications.
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Affiliation(s)
- Divya
S. Koshy
- TERI-Deakin
Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy
and Resources Institute, TERI Gram, Gwal
Pahari, Gurugram, Haryana 122001, India
- Institute
for Frontier Materials, Deakin University, Geelong Waurn Ponds Campus, Pigdons
Road, Geelong, VIC 3216, Australia
| | - Benjamin J. Allardyce
- Institute
for Frontier Materials, Deakin University, Geelong Waurn Ponds Campus, Pigdons
Road, Geelong, VIC 3216, Australia
| | - Ludovic F. Dumée
- Department
of Chemical Engineering, Khalifa University
of Science and Technology, Abu
Dhabi 127788, UAE
| | - Alessandra Sutti
- Institute
for Frontier Materials, Deakin University, Geelong Waurn Ponds Campus, Pigdons
Road, Geelong, VIC 3216, Australia
| | - Rangam Rajkhowa
- Institute
for Frontier Materials, Deakin University, Geelong Waurn Ponds Campus, Pigdons
Road, Geelong, VIC 3216, Australia
| | - Ruchi Agrawal
- TERI-Deakin
Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy
and Resources Institute, TERI Gram, Gwal
Pahari, Gurugram, Haryana 122001, India
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2
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Zhu T, Zhang X, Li R, Wu B. Efficient production of peptidylglycine α-hydroxylating monooxygenase in yeast for protein C-terminal functionalization. Int J Biol Macromol 2024; 263:130443. [PMID: 38417749 DOI: 10.1016/j.ijbiomac.2024.130443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Peptidylglycine α-hydroxylating monooxygenase (PHM) is pivotal for C-terminal amidation of bioactive peptides in animals, offering substantial potential for customized protein synthesis. However, efficient PHM production has been hindered by the complexity of animal cell culture and the absence of glycosylation in bacterial hosts. Here, we demonstrate the recombinant expression of Caenorhabditis elegans PHM in the yeast Pichia pastoris, achieving a remarkable space-time yield of 28.8 U/L/day. This breakthrough surpasses prior PHM production rates and eliminates the need for specialized cultivation equipment or complex transfection steps. Mass spectrometry revealed N-glycosylation at residue N182 of recombinant CePHM, which impacts the enzyme's activity as indicated by biochemical experiments. To showcase the utility of CePHM, we performed C-terminal amidation on ubiquitin at a substrate loading of 30 g/L, a concentration meeting the requirements for pharmaceutical peptide production. Overall, this work establishes an efficient PHM production method, promising advancements in scalable manufacturing of C-terminally modified bioactive peptides and probe proteins.
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Affiliation(s)
- Tong Zhu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanshuo Zhang
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruifeng Li
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Bian Wu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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3
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Zhu T, Sun J, Pang H, Wu B. Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation. JACS AU 2024; 4:788-797. [PMID: 38425901 PMCID: PMC10900485 DOI: 10.1021/jacsau.3c00792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
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Affiliation(s)
- Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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4
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Liu YD, Beardsley MI, Yang F. Expanding the Analytical Toolbox: Developing New Lys-C Peptide Mapping Methods with Minimized Assay-Induced Artifacts to Fully Characterize Antibodies. Pharmaceuticals (Basel) 2023; 16:1327. [PMID: 37765135 PMCID: PMC10536426 DOI: 10.3390/ph16091327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Peptide mapping is an important tool used to confirm that the correct sequence has been expressed for a protein and to evaluate protein post-translational modifications (PTMs) that may arise during the production, processing, or storage of protein drugs. Our new orally administered drug (Ab-1), a single-domain antibody, is highly stable and resistant to proteolysis. Analysis via the commonly used tryptic mapping method did not generate sufficient sequence coverage. Alternative methods were needed to study the Ab-1 drug substance (75 mg/mL) and drug product (3 mg/mL). To meet these analytical needs, we developed two new peptide mapping methods using lysyl endopeptidase (Lys-C) digestion. These newly developed protein digestion protocols do not require desalting/buffer-exchange steps, thereby reducing sample preparation time and improving method robustness. Additionally, the protein digestion is performed under neutral pH with methionine acting as a scavenger to minimize artifacts, such as deamidation and oxidation, which are induced during sample preparation. Further, the method for low-concentration samples performs comparably to the method for high-concentration samples. Both methods provide 100% sequence coverage for Ab-1, and, therefore, enable comprehensive characterization for its product quality attribute (PQA) assessment. Both methods can be used to study other antibody formats.
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Affiliation(s)
| | | | - Feng Yang
- Department of Protein Analytical Chemistry, Genentech/Roche, South San Francisco, CA 94080, USA; (Y.D.L.); (M.I.B.)
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5
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Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
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6
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Varnavides G, Madern M, Anrather D, Hartl N, Reiter W, Hartl M. In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods. J Proteome Res 2022; 21:2397-2411. [PMID: 36006919 PMCID: PMC9552232 DOI: 10.1021/acs.jproteome.2c00265] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Robust, efficient, and reproducible protein extraction
and sample
processing is a key step for bottom-up proteomics analyses. While
many sample preparation protocols for mass spectrometry have been
described, selecting an appropriate method remains challenging since
some protein classes may require specialized solubilization, precipitation,
and digestion procedures. Here, we present a comprehensive comparison
of the 16 most widely used sample preparation methods, covering in-solution
digests, device-based methods, and commercially available kits. We
find a remarkably good performance of the majority of the protocols
with high reproducibility, little method dependency, and low levels
of artifact formation. However, we revealed method-dependent differences
in the recovery of specific protein features, which we summarized
in a descriptive guide matrix. Our work thereby provides a solid basis
for the selection of MS sample preparation strategies for a given
proteomics project.
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Affiliation(s)
- Gina Varnavides
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Moritz Madern
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Dorothea Anrather
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Natascha Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Wolfgang Reiter
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
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7
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Garreto L, Charneau S, Mandacaru SC, Nóbrega OT, Motta FN, de Araújo CN, Tonet AC, Modesto FMB, Paula LM, de Sousa MV, Santana JM, Acevedo AC, Bastos IMD. Mapping Salivary Proteases in Sjögren's Syndrome Patients Reveals Overexpression of Dipeptidyl Peptidase-4/CD26. Front Immunol 2021; 12:686480. [PMID: 34220840 PMCID: PMC8247581 DOI: 10.3389/fimmu.2021.686480] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Sjögren's Syndrome (SS) is an autoimmune exocrinopathy characterized by the progressive damage of salivary and lacrimal glands associated with lymphocytic infiltration. Identifying new non-invasive biomarkers for SS diagnosis remains a challenge, and alterations in saliva composition reported in patients turn this fluid into a source of potential biomarkers. Among these, proteases are promising candidates since they are involved in several key physio-pathological processes. This study evaluated differentially expressed proteases in SS individuals' saliva using synthetic fluorogenic substrates, zymography, ELISA, and proteomic approaches. Here we reported, for the first time, increased activity of the serine protease dipeptidyl peptidase-4/CD26 (DPP4/CD26) in pSS saliva, the expression level of which was corroborated by ELISA assay. Gelatin zymograms showed that metalloproteinase proteolytic band profiles differed significantly in intensity between control and SS groups. Focusing on matrix metalloproteinase-9 (MMP9) expression, an increased tendency in pSS saliva (p = 0.0527) was observed compared to the control group. Samples of control, pSS, and sSS were analyzed by mass spectrometry to reveal a general panorama of proteases in saliva. Forty-eight protein groups of proteases were identified, among which were the serine proteases cathepsin G (CTSG), neutrophil elastase (ELANE), myeloblastin (PRTN3), MMP9 and several protease inhibitors. This work paves the way for proteases to be explored in the future as biomarkers, emphasizing DPP4 by its association in several autoimmune and inflammatory diseases. Besides its proteolytic role, DPP4/CD26 acts as a cell surface receptor, signal transduction mediator, adhesion and costimulatory protein involved in T lymphocytes activation.
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Affiliation(s)
- Laís Garreto
- Pathogen–Host Interface Laboratory, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Sébastien Charneau
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Samuel Coelho Mandacaru
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | | | - Flávia N. Motta
- Pathogen–Host Interface Laboratory, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
- Faculty of Ceilândia, University of Brasília, Brasília, Brazil
| | - Carla N. de Araújo
- Pathogen–Host Interface Laboratory, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
- Faculty of Ceilândia, University of Brasília, Brasília, Brazil
| | - Audrey C. Tonet
- Laboratory of Immune Gerontology, Catholic University of Brasília, Brasília, Brazil
| | | | - Lilian M. Paula
- Laboratory of Oral Histopathology, Department of Odontology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Jaime M. Santana
- Pathogen–Host Interface Laboratory, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Ana Carolina Acevedo
- Laboratory of Oral Histopathology, Department of Odontology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Izabela M. D. Bastos
- Pathogen–Host Interface Laboratory, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
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8
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Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res 2020; 19:1183-1195. [PMID: 32027144 DOI: 10.1021/acs.jproteome.9b00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate protein activity. We implemented and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine time points. We report that basic-pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2275 proteins across three biological replicates and found that differential expression peaked near 90 min following heat shock (with 868 differentially expressed proteins at 5% false discovery rate). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rebecca E Hardman
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas 72701, United States.,Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rick D Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jeffrey A Lewis
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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9
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Proteomic Characterization of the Heart and Skeletal Muscle Reveals Widespread Arginine ADP-Ribosylation by the ARTC1 Ectoenzyme. Cell Rep 2019; 24:1916-1929.e5. [PMID: 30110646 DOI: 10.1016/j.celrep.2018.07.048] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/19/2018] [Accepted: 07/12/2018] [Indexed: 01/05/2023] Open
Abstract
The clostridium-like ecto-ADP-ribosyltransferase ARTC1 is expressed in a highly restricted manner in skeletal muscle and heart tissue. Although ARTC1 is well studied, the identification of ARTC1 targets in vivo and subsequent characterization of ARTC1-regulated cellular processes on the proteome level have been challenging and only a few ARTC1-ADP-ribosylated targets are known. Applying our recently developed mass spectrometry-based workflow to C2C12 myotubes and to skeletal muscle and heart tissues from wild-type mice, we identify hundreds of ARTC1-ADP-ribosylated proteins whose modifications are absent in the ADP-ribosylome of ARTC1-deficient mice. These proteins are ADP-ribosylated on arginine residues and mainly located on the cell surface or in the extracellular space. They are associated with signal transduction, transmembrane transport, and muscle function. Validation of hemopexin (HPX) as a ARTC1-target protein confirmed the functional importance of ARTC1-mediated extracellular arginine ADP-ribosylation at the systems level.
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10
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Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell 2019; 179:543-560.e26. [DOI: 10.1016/j.cell.2019.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/20/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022]
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11
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Hakobyan A, Schneider MB, Liesack W, Glatter T. Efficient Tandem LysC/Trypsin Digestion in Detergent Conditions. Proteomics 2019; 19:e1900136. [DOI: 10.1002/pmic.201900136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/22/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Anna Hakobyan
- Research group of Methanotrophic Bacteria, and Environmental Genomics/TranscriptomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
| | - Martin Bernd Schneider
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
- Genomics and Proteomics Core FacilityGerman Cancer Research Center Im Neuenheimer Feld 580 D‐69120 Heidelberg Germany
| | - Werner Liesack
- Research group of Methanotrophic Bacteria, and Environmental Genomics/TranscriptomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
- Center for Synthetic Microbiology (SYNMIKRO)Philipps‐Universität Marburg Karl‐von‐Frisch‐Str. 16 D‐35043 Marburg Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
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12
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Lau BYC, Othman A. Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis. PLoS One 2019; 14:e0221052. [PMID: 31415606 PMCID: PMC6695131 DOI: 10.1371/journal.pone.0221052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/29/2019] [Indexed: 11/29/2022] Open
Abstract
Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was insignificant. A deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had increased the number of identified proteins from oil palm mesocarps, enriched their gene ontologies and reduced the number of carbamylated lysine residues by more than 67.0%, compared to urea/thiourea/CHAPS buffer. Although only 62.0% of the total identified proteins were shared between the urea/thiourea/CHAPS and sodium deoxycholate buffers, the importance of the remaining 38.0% proteins depends on the applications. The only observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and but it could be easily rectified through a 4-fold dilution. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps with higher efficiency compared to urea/thiourea/CHAPS buffer. The sodium deoxycholate buffer is more favorable for proteomics analysis due to its proven advantages over urea/thiourea/CHAPS buffer.
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Affiliation(s)
- Benjamin Yii Chung Lau
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Abrizah Othman
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
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13
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Batth TS, Tollenaere MX, Rüther P, Gonzalez-Franquesa A, Prabhakar BS, Bekker-Jensen S, Deshmukh AS, Olsen JV. Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation. Mol Cell Proteomics 2019; 18:1027-1035. [PMID: 30833379 PMCID: PMC6495262 DOI: 10.1074/mcp.tir118.001270] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/26/2019] [Indexed: 11/06/2022] Open
Abstract
Universal proteomics sample preparation is challenging because of the high heterogeneity of biological samples. Here we describe a novel mechanism that exploits the inherent instability of denatured proteins for nonspecific immobilization on microparticles by protein aggregation capture. To demonstrate the general applicability of this mechanism, we analyzed phosphoproteomes, tissue proteomes, and interaction proteomes as well as dilute secretomes. The findings present a practical, sensitive and cost-effective proteomics sample preparation method.
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Affiliation(s)
- Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - MaximA X Tollenaere
- Cellular Stress Signaling Group, Center for Healthy Aging, University of Copenhagen, Denmark
| | - Patrick Rüther
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Alba Gonzalez-Franquesa
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark;; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Bhargav S Prabhakar
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Cellular Stress Signaling Group, Center for Healthy Aging, University of Copenhagen, Denmark
| | - Atul S Deshmukh
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark;.
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14
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Gan Y, Xiao Y, Wang S, Guo H, Liu M, Wang Z, Wang Y. Protein-Based Fingerprint Analysis for the Identification of Ranae Oviductus Using RP-HPLC. Molecules 2019; 24:E1687. [PMID: 31052194 PMCID: PMC6539769 DOI: 10.3390/molecules24091687] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 01/14/2023] Open
Abstract
This work demonstrated a method combining reversed-phase high-performance liquid chromatography (RP-HPLC) with chemometrics analysis to identify the authenticity of Ranae Oviductus. The fingerprint chromatograms of the Ranae Oviductus protein were established through an Agilent Zorbax 300SB-C8 column and diode array detection at 215 nm, using 0.085% TFA (v/v) in acetonitrile (A) and 0.1% TFA in ultrapure water (B) as mobile phase. The similarity was in the range of 0.779-0.980. The fingerprint chromatogram of Ranae Oviductus showed a significant difference with counterfeit products. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) successfully identified Ranae Oviductus from the samples. These results indicated that the method established in this work was reliable.
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Affiliation(s)
- Yuanshuai Gan
- College of Pharmacy, Jilin University, Changchun 130021, China.
| | - Yao Xiao
- College of Pharmacy, Jilin University, Changchun 130021, China.
| | - Shihan Wang
- College of Chinese Herbal Medicine, Jilin Agricultural University, Changchun 130118, China.
| | - Hongye Guo
- College of Pharmacy, Jilin University, Changchun 130021, China.
| | - Min Liu
- College of Pharmacy, Jilin University, Changchun 130021, China.
| | - Zhihan Wang
- Department of Physical Sciences, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Yongsheng Wang
- College of Pharmacy, Jilin University, Changchun 130021, China.
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15
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Vincent D, Rochfort S, Spangenberg G. Optimisation of Protein Extraction from Medicinal Cannabis Mature Buds for Bottom-Up Proteomics. Molecules 2019; 24:molecules24040659. [PMID: 30781766 PMCID: PMC6412734 DOI: 10.3390/molecules24040659] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 11/17/2022] Open
Abstract
Medicinal cannabis is used to relieve the symptoms of certain medical conditions, such as epilepsy. Cannabis is a controlled substance and until recently was illegal in many jurisdictions. Consequently, the study of this plant has been restricted. Proteomics studies on Cannabis sativa reported so far have been primarily based on plant organs and tissues other than buds, such as roots, hypocotyl, leaves, hempseeds and flour. As far as we know, no optimisation of protein extraction from cannabis reproductive tissues has been attempted. Therefore, we set out to assess different protein extraction methods followed by mass spectrometry-based proteomics to recover, separate and identify the proteins of the reproductive organs of medicinal cannabis, apical buds and isolated trichomes. Database search following shotgun proteomics was limited to protein sequences from C. sativa and closely related species available from UniprotKB. Our results demonstrate that a buffer containing the chaotrope reagent guanidine hydrochloride recovers many more proteins than a urea-based buffer. In combination with a precipitation with trichloroacetic acid, such buffer proved optimum to identify proteins using a trypsin digestion followed by nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) analyses. This is validated by focusing on enzymes involved in the phytocannabinoid pathway.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - Simone Rochfort
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
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16
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Marshall NC, Klein T, Thejoe M, von Krosigk N, Kizhakkedathu J, Finlay BB, Overall CM. Global Profiling of Proteolysis from the Mitochondrial Amino Terminome during Early Intrinsic Apoptosis Prior to Caspase-3 Activation. J Proteome Res 2018; 17:4279-4296. [PMID: 30371095 DOI: 10.1021/acs.jproteome.8b00675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human genome encodes ∼20 mitochondrial proteases, yet we know little of how they sculpt the mitochondrial proteome, particularly during important mitochondrial events such as the initiation of apoptosis. To characterize global mitochondrial proteolysis we refined our technique, terminal amine isotopic labeling of substrates, for mitochondrial SILAC (MS-TAILS) to identify proteolysis across mitochondria and parent cells in parallel. Our MS-TAILS analyses identified 45% of the mitochondrial proteome and identified protein amino (N)-termini from 26% of mitochondrial proteins, the highest reported coverage of the human mitochondrial N-terminome. MS-TAILS revealed 97 previously unknown proteolytic sites. MS-TAILS also identified mitochondrial targeting sequence (MTS) removal by proteolysis during protein import, confirming 101 MTS sites and identifying 135 new MTS sites, revealing a wobbly requirement for the MTS cleavage motif. To examine the relatively unknown initial cleavage events occurring before the well-studied activation of caspase-3 in intrinsic apoptosis, we quantitatively compared N-terminomes of mitochondria and their parent cells before and after initiation of apoptosis at very early time points. By identifying altered levels of >400 N-termini, MS-TAILS analyses implicated specific mitochondrial pathways including protein import, fission, and iron homeostasis in apoptosis initiation. Notably, both staurosporine and Bax activator molecule-7 triggered in common 7 mitochondrial and 85 cellular cleavage events that are potentially part of an essential core of apoptosis-initiating events. All mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD009054.
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Affiliation(s)
- Natalie C Marshall
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | | | - Maichael Thejoe
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Niklas von Krosigk
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Jayachandran Kizhakkedathu
- Department of Pathology and Laboratory Medicine and Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z2 , Canada
| | - B Brett Finlay
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
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17
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Iliuk A. Identification of Phosphorylated Proteins on a Global Scale. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2018; 10:e48. [PMID: 29927094 PMCID: PMC6125197 DOI: 10.1002/cpch.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) has enabled researchers to analyze complex biological samples with unprecedented depth. It facilitates the identification and quantification of modifications within thousands of proteins in a single large-scale proteomic experiment. Analysis of phosphorylation, one of the most common and important post-translational modifications, has particularly benefited from such progress in the field. Here, detailed protocols are provided for a few well-regarded, common sample preparation methods for an effective phosphoproteomic experiment. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Anton Iliuk
- Tymora Analytical Operations, Innovations, West Lafayette, Indiana
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18
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UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nat Struct Mol Biol 2018; 25:631-640. [PMID: 29967540 DOI: 10.1038/s41594-018-0084-y] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
Abstract
Ubiquitination is a post-translational modification (PTM) that is essential for balancing numerous physiological processes. To enable delineation of protein ubiquitination at a site-specific level, we generated an antibody, denoted UbiSite, recognizing the C-terminal 13 amino acids of ubiquitin, which remain attached to modified peptides after proteolytic digestion with the endoproteinase LysC. Notably, UbiSite is specific to ubiquitin. Furthermore, besides ubiquitination on lysine residues, protein N-terminal ubiquitination is readily detected as well. By combining UbiSite enrichment with sequential LysC and trypsin digestion and high-accuracy MS, we identified over 63,000 unique ubiquitination sites on 9,200 proteins in two human cell lines. In addition to uncovering widespread involvement of this PTM in all cellular aspects, the analyses reveal an inverse association between protein N-terminal ubiquitination and acetylation, as well as a complete lack of correlation between changes in protein abundance and alterations in ubiquitination sites upon proteasome inhibition.
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19
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Site-specific characterization of endogenous SUMOylation across species and organs. Nat Commun 2018; 9:2456. [PMID: 29942033 PMCID: PMC6018634 DOI: 10.1038/s41467-018-04957-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/05/2018] [Indexed: 12/30/2022] Open
Abstract
Small ubiquitin-like modifiers (SUMOs) are post-translational modifications that play crucial roles in most cellular processes. While methods exist to study exogenous SUMOylation, large-scale characterization of endogenous SUMO2/3 has remained technically daunting. Here, we describe a proteomics approach facilitating system-wide and in vivo identification of lysines modified by endogenous and native SUMO2. Using a peptide-level immunoprecipitation enrichment strategy, we identify 14,869 endogenous SUMO2/3 sites in human cells during heat stress and proteasomal inhibition, and quantitatively map 1963 SUMO sites across eight mouse tissues. Characterization of the SUMO equilibrium highlights striking differences in SUMO metabolism between cultured cancer cells and normal tissues. Targeting preferences of SUMO2/3 vary across different organ types, coinciding with markedly differential SUMOylation states of all enzymes involved in the SUMO conjugation cascade. Collectively, our systemic investigation details the SUMOylation architecture across species and organs and provides a resource of endogenous SUMOylation sites on factors important in organ-specific functions. Proteomics is a powerful method to study protein SUMOylation, but system-wide insights into endogenous SUMO2/3 modification events are still sparse. Here, the authors develop a more sensitive SUMO proteomics approach, providing detailed maps of endogenous SUMO2/3 sites in human cells and mouse tissues.
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20
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Larsen SC, Leutert M, Bilan V, Martello R, Jungmichel S, Young C, Hottiger MO, Nielsen ML. Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2018; 1608:149-162. [PMID: 28695509 DOI: 10.1007/978-1-4939-6993-7_11] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ADP-ribosylation is a posttranslational modification (PTM) that affects a variety of cellular processes. In recent years, mass spectrometry (MS)-based proteomics has become a valuable tool for studying ADP-ribosylation. However, studying this PTM in vivo in an unbiased and sensitive manner has remained a difficult challenge. Here, we describe a detailed protocol for unbiased analysis of ADP-ribosylated proteins and their ADP-ribose acceptor sites under physiological conditions. The method relies on the enrichment of mono-ADP-ribosylated peptides using the macrodomain Af1521 in combination with liquid chromatography-high-resolution tandem MS (LC-MS/MS). The 5-day protocol explains the step-by-step enrichment and identification of ADP-ribosylated peptides from cell culture stage all the way through to data processing using the MaxQuant software suite.
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Affiliation(s)
- Sara C Larsen
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Mario Leutert
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich/ETH Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Vera Bilan
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich/ETH Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rita Martello
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Stephanie Jungmichel
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Clifford Young
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael L Nielsen
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark.
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21
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Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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22
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Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV. Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics. J Proteome Res 2017; 17:727-738. [DOI: 10.1021/acs.jproteome.7b00602] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian D. Kelstrup
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Dorte B. Bekker-Jensen
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Tabiwang N. Arrey
- Thermo Fisher Scientific, Hanna-Kunath-Straße
11, Bremen 28199, Germany
| | - Alexander Hogrebe
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Alexander Harder
- Thermo Fisher Scientific, Hanna-Kunath-Straße
11, Bremen 28199, Germany
| | - Jesper V. Olsen
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
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23
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Abplanalp J, Leutert M, Frugier E, Nowak K, Feurer R, Kato J, Kistemaker HVA, Filippov DV, Moss J, Caflisch A, Hottiger MO. Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nat Commun 2017; 8:2055. [PMID: 29234005 PMCID: PMC5727137 DOI: 10.1038/s41467-017-02253-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/15/2017] [Indexed: 11/09/2022] Open
Abstract
ADP-ribosylation is a posttranslational modification that exists in monomeric and polymeric forms. Whereas the writers (e.g. ARTD1/PARP1) and erasers (e.g. PARG, ARH3) of poly-ADP-ribosylation (PARylation) are relatively well described, the enzymes involved in mono-ADP-ribosylation (MARylation) have been less well investigated. While erasers for the MARylation of glutamate/aspartate and arginine have been identified, the respective enzymes with specificity for serine were missing. Here we report that, in vitro, ARH3 specifically binds and demodifies proteins and peptides that are MARylated. Molecular modeling and site-directed mutagenesis of ARH3 revealed that numerous residues are critical for both the mono- and the poly-ADP-ribosylhydrolase activity of ARH3. Notably, a mass spectrometric approach showed that ARH3-deficient mouse embryonic fibroblasts are characterized by a specific increase in serine-ADP-ribosylation in vivo under untreated conditions as well as following hydrogen peroxide stress. Together, our results establish ARH3 as a serine mono-ADP-ribosylhydrolase and as an important regulator of the basal and stress-induced ADP-ribosylome.
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Affiliation(s)
- Jeannette Abplanalp
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mario Leutert
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Emilie Frugier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Roxane Feurer
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jiro Kato
- Laboratory of Translational Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, 20892-1590, USA
| | - Hans V A Kistemaker
- Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Joel Moss
- Laboratory of Translational Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, 20892-1590, USA
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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24
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Mullari M, Lyon D, Jensen LJ, Nielsen ML. Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. J Proteome Res 2017. [PMID: 28648085 DOI: 10.1021/acs.jproteome.7b00042] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level. However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (pCLAP) that allows rapid characterization of RNA-binding regions in proteins. pCLAP is based upon the combined use of UV cross-linking and enzymatic digestion of RNA-bound proteins followed by single-shot mass spectrometric analysis. To benchmark our method, we identified the binding regions for polyadenylated RNA-binding proteins in HEK293 cells, allowing us to map the mRNA interaction regions of more than 1000 RBPs with very high reproducibility from replicate single-shot analyses. Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the specificity of our approach.
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Affiliation(s)
- Meeli Mullari
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - David Lyon
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
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25
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Ashraf Kharaz Y, Zamboulis D, Sanders K, Comerford E, Clegg P, Peffers M. Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis. Proteomics 2017; 17:1700018. [PMID: 28547889 PMCID: PMC5575552 DOI: 10.1002/pmic.201700018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 01/12/2023]
Abstract
Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest™, and their combinations for shotgun mass spectrometry. An initial proteomic analysis was performed following urea, GnHCl, and RapiGest™ extraction of equine superficial digital flexor tendon (SDFT) tissue. Subsequently, another proteomic analysis was performed following extraction with GnHCl, Rapigest™, and their combinations. Between the two chaotropic agents, GnHCl extracted more proteins, whilst a greater number of proteins were solely identified after Rapigest™ extraction. Protein extraction with a combination of GnHCl followed by RapiGest™ on the insoluble pellet demonstrated, after label-free quantification, increased abundance of identified collagen proteins and low sample to sample variability. In contrast, GnHCl extraction on its own showed increased abundance of identified proteoglycans and cellular proteins. Therefore, the selection of protein extraction method for tendon tissue for mass spectrometry analysis should reflect the focus of the study.
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Affiliation(s)
- Yalda Ashraf Kharaz
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Danae Zamboulis
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Karen Sanders
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Eithne Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Peter Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
| | - Mandy Peffers
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
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26
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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27
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Analysis of Conformational Stability of Abnormal Prion Protein Aggregates across the Spectrum of Creutzfeldt-Jakob Disease Prions. J Virol 2016; 90:6244-6254. [PMID: 27122583 DOI: 10.1128/jvi.00144-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/21/2016] [Indexed: 01/24/2023] Open
Abstract
UNLABELLED The wide phenotypic variability of prion diseases is thought to depend on the interaction of a host genotype with prion strains that have self-perpetuating biological properties enciphered in distinct conformations of the misfolded prion protein PrP(Sc) This concept is largely based on indirect approaches studying the effect of proteases or denaturing agents on the physicochemical properties of PrP(Sc) aggregates. Furthermore, most data come from studies on rodent-adapted prion strains, making current understanding of the molecular basis of strains and phenotypic variability in naturally occurring diseases, especially in humans, more limited. To fill this gap, we studied the effects of guanidine hydrochloride (GdnHCl) and heating on PrP(Sc) aggregates extracted from 60 sporadic Creutzfeldt-Jakob disease (CJD) and 6 variant CJD brains. While denaturation curves obtained after exposure of PrP(Sc) to increasing GdnHCl concentrations showed similar profiles among the 7 CJD types analyzed, PrP(Sc) exposure to increasing temperature revealed significantly different and type-specific responses. In particular, MM1 and VV2, the most prevalent and fast-replicating CJD types, showed stable and highly resistant PrP(Sc) aggregates, whereas VV1, a rare and slowly propagating type, revealed unstable aggregates that easily dissolved at low temperature. Taken together, our results indicate that the molecular interactions mediating the aggregation state of PrP(Sc), possibly enciphering strain diversity, are differently targeted by GdnHCl, temperature, and proteases. Furthermore, the detected positive correlation between the thermostability of PrP(Sc) aggregates and disease transmission efficiency makes inconsistent the proposed hypothesis that a decrease in conformational stability of prions results in an increase in their replication efficiency. IMPORTANCE Prion strains are defined as infectious isolates propagating distinctive phenotypic traits after transmission to syngeneic hosts. Although the molecular basis of prion strains is not fully understood, it is largely accepted that variations in prion protein conformation drive the molecular changes leading to the different phenotypes. In this study, we exposed abnormal prion protein aggregates encompassing the spectrum of human prion strains to both guanidine hydrochloride and thermal unfolding. Remarkably, while exposure to increasing temperature revealed significant strain-specific differences in the denaturation profile of the protein, treatment with guanidine hydrochloride did not. The findings suggest that thermal and chemical denaturation perturb the structure of prion protein aggregates differently. Moreover, since the most thermostable prion protein types were those associated with the most prevalent phenotypes and most rapidly and efficiently transmitting strains, the results suggest a direct correlation between strain replication efficiency and the thermostability of prion protein aggregates.
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Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology. Proteomes 2016; 4:proteomes4010006. [PMID: 28248217 PMCID: PMC5217365 DOI: 10.3390/proteomes4010006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence, of altered protein expressions profiles and/or their posttranslational modifications (PTMs). Mass spectrometry (MS)-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle proteomics are challenging. This review describes the technical limitations of skeletal muscle proteomics as well as emerging developments in proteomics workflow with respect to samples preparation, liquid chromatography (LC), MS and computational analysis. These technologies have not yet been fully exploited in the field of skeletal muscle proteomics. Future studies that involve state-of-the-art proteomics technology will broaden our understanding of exercise-induced adaptations as well as molecular pathogenesis of insulin resistance. This could lead to the identification of new therapeutic targets.
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Jersie-Christensen RR, Sultan A, Olsen JV. Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity. Methods Mol Biol 2016; 1355:251-260. [PMID: 26584931 DOI: 10.1007/978-1-4939-3049-4_17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched using TiO2 beads and the orbitrap mass spectrometer is operated in a sensitive mode with higher energy collisional dissociation (HCD).
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Affiliation(s)
- Rosa R Jersie-Christensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Abida Sultan
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
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30
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Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p. Nat Commun 2015; 6:7726. [PMID: 26158509 PMCID: PMC4510963 DOI: 10.1038/ncomms8726] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 06/04/2015] [Indexed: 01/23/2023] Open
Abstract
The essential vitamin biotin is a covalent and tenaciously attached prosthetic group in several carboxylases that play important roles in the regulation of energy metabolism. Here we describe increased acetyl-CoA levels and mitochondrial hyperacetylation as downstream metabolic effects of biotin deficiency. Upregulated mitochondrial acetylation sites correlate with the cellular deficiency of the Hst4p deacetylase, and a biotin-starvation-induced accumulation of Hst4p in mitochondria supports a role for Hst4p in lowering mitochondrial acetylation. We show that biotin starvation and knockout of Hst4p cause alterations in cellular respiration and an increase in reactive oxygen species (ROS). These results suggest that Hst4p plays a pivotal role in biotin metabolism and cellular energy homeostasis, and supports that Hst4p is a functional yeast homologue of the sirtuin deacetylase SIRT3. With biotin deficiency being involved in various metabolic disorders, this study provides valuable insight into the metabolic effects biotin exerts on eukaryotic cells.
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31
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Mathiassen SG, Larsen IB, Poulsen EG, Madsen CT, Papaleo E, Lindorff-Larsen K, Kragelund BB, Nielsen ML, Kriegenburg F, Hartmann-Petersen R. A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast. J Biol Chem 2015; 290:21141-21153. [PMID: 26152728 DOI: 10.1074/jbc.m115.662312] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/30/2022] Open
Abstract
A mutation, L166P, in the cytosolic protein, PARK7/DJ-1, causes protein misfolding and is linked to Parkinson disease. Here, we identify the fission yeast protein Sdj1 as the orthologue of DJ-1 and calculate by in silico saturation mutagenesis the effects of point mutants on its structural stability. We also map the degradation pathways for Sdj1-L169P, the fission yeast orthologue of the disease-causing DJ-1 L166P protein. Sdj1-L169P forms inclusions, which are enriched for the Hsp104 disaggregase. Hsp104 and Hsp70-type chaperones are required for efficient degradation of Sdj1-L169P. This also depends on the ribosome-associated E3 ligase Ltn1 and its co-factor Rqc1. Although Hsp104 is absolutely required for proteasomal degradation of Sdj1-L169P aggregates, the degradation of already aggregated Sdj1-L169P occurs independently of Ltn1 and Rqc1. Thus, our data point to soluble Sdj1-L169P being targeted early by Ltn1 and Rqc1. The fraction of Sdj1-L169P that escapes this first inspection then forms aggregates that are subsequently cleared via an Hsp104- and proteasome-dependent pathway.
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Affiliation(s)
- Søs G Mathiassen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ida B Larsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Esben G Poulsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Christian T Madsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Elena Papaleo
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Franziska Kriegenburg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Rasmus Hartmann-Petersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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32
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Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M. A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day. Mol Cell Proteomics 2015; 14:2030-41. [PMID: 25887394 PMCID: PMC4587330 DOI: 10.1074/mcp.o115.049460] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 12/12/2022] Open
Abstract
The field of proteomics has evolved hand-in-hand with technological advances in LC-MS/MS systems, now enabling the analysis of very deep proteomes in a reasonable time. However, most applications do not deal with full cell or tissue proteomes but rather with restricted subproteomes relevant for the research context at hand or resulting from extensive fractionation. At the same time, investigation of many conditions or perturbations puts a strain on measurement capacity. Here, we develop a high-throughput workflow capable of dealing with large numbers of low or medium complexity samples and specifically aim at the analysis of 96-well plates in a single day (15 min per sample). We combine parallel sample processing with a modified liquid chromatography platform driving two analytical columns in tandem, which are coupled to a quadrupole Orbitrap mass spectrometer (Q Exactive HF). The modified LC platform eliminates idle time between measurements, and the high sequencing speed of the Q Exactive HF reduces required measurement time. We apply the pipeline to the yeast chromatin remodeling landscape and demonstrate quantification of 96 pull-downs of chromatin complexes in about 1 day. This is achieved with only 500 μg input material, enabling yeast cultivation in a 96-well format. Our system retrieved known complex-members and the high throughput allowed probing with many bait proteins. Even alternative complex compositions were detectable in these very short gradients. Thus, sample throughput, sensitivity and LC/MS-MS duty cycle are improved severalfold compared with established workflows. The pipeline can be extended to different types of interaction studies and to other medium complexity proteomes.
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Affiliation(s)
- Fabian Hosp
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Richard A Scheltema
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - H Christian Eberl
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nils A Kulak
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Eva C Keilhauer
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Korbinian Mayr
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Rakus D, Gizak A, Deshmukh A, Wiśniewski JR. Absolute quantitative profiling of the key metabolic pathways in slow and fast skeletal muscle. J Proteome Res 2015; 14:1400-11. [PMID: 25597705 DOI: 10.1021/pr5010357] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Slow and fast skeletal muscles are composed of, respectively, mainly oxidative and glycolytic muscle fibers, which are the basic cellular motor units of the motility apparatus. They largely differ in excitability, contraction mechanism, and metabolism. Because of their pivotal role in body motion and homeostasis, the skeletal muscles have been extensively studied using biochemical and molecular biology approaches. Here we describe a simple analytical and computational approach to estimate titers of enzymes of basic metabolic pathways and proteins of the contractile machinery in the skeletal muscles. Proteomic analysis of mouse slow and fast muscles allowed estimation of the titers of enzymes involved in the carbohydrate, lipid, and energy metabolism. Notably, we observed that differences observed between the two muscle types occur simultaneously for all proteins involved in a specific process such as glycolysis, free fatty acid catabolism, Krebs cycle, or oxidative phosphorylation. These differences are in a good agreement with the well-established biochemical picture of the muscle types. We show a correlation between maximal activity and the enzyme titer, suggesting that change in enzyme concentration is a good proxy for its catalytic potential in vivo. As a consequence, proteomic profiling of enzyme titers can be used to monitor metabolic changes in cells. Additionally, quantitative data of structural proteins allowed studying muscle type specific cell architecture and its remodeling. The presented proteomic approach can be applied to study metabolism in any other tissue or cell line.
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Affiliation(s)
- Dariusz Rakus
- Department of Animal Molecular Physiology, Wroclaw University , Wroclaw 50-205, Poland
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Kelstrup CD, Jersie-Christensen RR, Batth TS, Arrey TN, Kuehn A, Kellmann M, Olsen JV. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. J Proteome Res 2014; 13:6187-95. [DOI: 10.1021/pr500985w] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christian D. Kelstrup
- Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Rosa R. Jersie-Christensen
- Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Tanveer S. Batth
- Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Tabiwang N. Arrey
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany
| | - Andreas Kuehn
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany
| | - Markus Kellmann
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany
| | - Jesper V. Olsen
- Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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Keilhauer EC, Hein MY, Mann M. Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics 2014; 14:120-35. [PMID: 25363814 PMCID: PMC4288248 DOI: 10.1074/mcp.m114.041012] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein–protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein–protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers.
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Affiliation(s)
- Eva C Keilhauer
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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36
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J. D'Souza RC, Knittle AM, Nagaraj N, van Dinther M, Choudhary C, ten Dijke P, Mann M, Sharma K. Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-. Sci Signal 2014; 7:rs5. [DOI: 10.1126/scisignal.2004856] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 2014; 11:319-24. [PMID: 24487582 DOI: 10.1038/nmeth.2834] [Citation(s) in RCA: 1166] [Impact Index Per Article: 116.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS)-based proteomics typically employs multistep sample-preparation workflows that are subject to sample contamination and loss. We report an in-StageTip method for performing sample processing, from cell lysis through elution of purified peptides, in a single, enclosed volume. This robust and scalable method largely eliminates contamination or loss. Peptides can be eluted in several fractions or in one step for single-run proteome analysis. In one day, we obtained the largest proteome coverage to date for budding and fission yeast, and found that protein copy numbers in these cells were highly correlated (R(2) = 0.78). Applying the in-StageTip method to quadruplicate measurements of a human cell line, we obtained copy-number estimates for 9,667 human proteins and observed excellent quantitative reproducibility between replicates (R(2) = 0.97). The in-StageTip method is straightforward and generally applicable in biological or clinical applications.
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