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Mun H, Lee S, Choi S, Jeong JH, Ko S, Chun YL, Deaton B, Yeager CT, Boyette A, Palmera J, Newman L, Zhou P, Shin S, Kim DC, Sagum CA, Bedford MT, Kim YK, Kwon J, Jung J, Chang JH, Yoon JH. Targeting of CYP2E1 by miRNAs in alcohol-induced intestine injury. Mol Cells 2024; 47:100074. [PMID: 38901530 PMCID: PMC11267015 DOI: 10.1016/j.mocell.2024.100074] [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: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Although binge alcohol-induced gut leakage has been studied extensively in the context of reactive oxygen species-mediated signaling, it was recently revealed that post-transcriptional regulation plays an essential role as well. Ethanol (EtOH)-inducible cytochrome P450-2E1 (CYP2E1), a key enzyme in EtOH metabolism, promotes alcohol-induced hepatic steatosis and inflammatory liver disease, at least in part by mediating changes in intestinal permeability. For instance, gut leakage and elevated intestinal permeability to endotoxins have been shown to be regulated by enhancing CYP2E1 mRNA and CYP2E1 protein levels. Although it is understood that EtOH promotes CYP2E1 induction and activation, the mechanisms that regulate CYP2E1 expression in the context of intestinal damage remain poorly defined. Specific miRNAs, including miR-132, miR-212, miR-378, and miR-552, have been shown to repress the expression of CYP2E1, suggesting that these miRNAs contribute to EtOH-induced intestinal injury. Here, we have shown that CYP2E1 expression is regulated post-transcriptionally through miRNA-mediated degradation, as follows: (1) the RNA-binding protein AU-binding factor 1 (AUF1) binds mature miRNAs, including CYP2E1-targeting miRNAs, and this binding modulates the degradation of corresponding target mRNAs upon EtOH treatment; (2) the serine/threonine kinase mammalian Ste20-like kinase 1 (MST1) mediates oxidative stress-induced phosphorylation of AUF1. Those findings suggest that reactive oxygen species-mediated signaling modulates AUF1/miRNA interaction through MST1-mediated phosphorylation. Thus, our study demonstrates the critical functions of AUF1 phosphorylation by MST1 in the decay of miRNAs targeting CYP2E1, the stabilization of CYP2E1 mRNA in the presence of EtOH, and the relationship of this pathway to subsequent intestinal injury.
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Affiliation(s)
- Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Sungyul Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Suyoung Choi
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Ji-Hoon Jeong
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yoo Lim Chun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Benjamin Deaton
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Clay T Yeager
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Audrey Boyette
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Juliana Palmera
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - London Newman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ping Zhou
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Soona Shin
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Dong-Chan Kim
- Division of Medical Device R&D Center, NQ-Lab, Inc.,Yongin-si, Gyeonggi-do 16827, Republic of Korea
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
| | - Jaeyul Kwon
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Education, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Translational Immunology Institute, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Junyang Jung
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA.
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2
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Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nat Methods 2024; 21:635-647. [PMID: 38532014 PMCID: PMC11009110 DOI: 10.1038/s41592-024-02211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.
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Affiliation(s)
- Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Guangzhou National Laboratory, Guang Zhou, China
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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3
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Ferrada E, Wiedmer T, Wang WA, Frommelt F, Steurer B, Klimek C, Lindinger S, Osthushenrich T, Garofoli A, Brocchetti S, Bradberry S, Huang J, MacNamara A, Scarabottolo L, Ecker GF, Malarstig A, Superti-Furga G. Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8. J Mol Biol 2024; 436:168383. [PMID: 38070861 DOI: 10.1016/j.jmb.2023.168383] [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: 08/22/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Creatine is an essential metabolite for the storage and rapid supply of energy in muscle and nerve cells. In humans, impaired metabolism, transport, and distribution of creatine throughout tissues can cause varying forms of mental disability, also known as creatine deficiency syndrome (CDS). So far, 80 mutations in the creatine transporter (SLC6A8) have been associated to CDS. To better understand the effect of human genetic variants on the physiology of SLC6A8 and their possible impact on CDS, we studied 30 missense variants including 15 variants of unknown significance, two of which are reported here for the first time. We expressed these variants in HEK293 cells and explored their subcellular localization and transport activity. We also applied computational methods to predict variant effect and estimate site-specific changes in thermodynamic stability. To explore variants that might have a differential effect on the transporter's conformers along the transport cycle, we constructed homology models of the inward facing, and outward facing conformations. In addition, we used mass-spectrometry to study proteins that interact with wild type SLC6A8 and five selected variants in HEK293 cells. In silico models of the protein complexes revealed how two variants impact the interaction interface of SLC6A8 with other proteins and how pathogenic variants lead to an enrichment of ER protein partners. Overall, our integrated analysis disambiguates the pathogenicity of 15 variants of unknown significance revealing diverse mechanisms of pathogenicity, including two previously unreported variants obtained from patients suffering from the creatine deficiency syndrome.
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Affiliation(s)
- Evandro Ferrada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Wen-An Wang
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Barbara Steurer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jiahui Huang
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | | | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Anders Malarstig
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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4
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Iannotta L, Emanuele M, Favetta G, Tombesi G, Vandewynckel L, Lara Ordóñez AJ, Saliou JM, Drouyer M, Sibran W, Civiero L, Nichols RJ, Athanasopoulos PS, Kortholt A, Chartier-Harlin MC, Greggio E, Taymans JM. PAK6-mediated phosphorylation of PPP2R2C regulates LRRK2-PP2A complex formation. Front Mol Neurosci 2023; 16:1269387. [PMID: 38169846 PMCID: PMC10759229 DOI: 10.3389/fnmol.2023.1269387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of inherited and sporadic Parkinson's disease (PD) and previous work suggests that dephosphorylation of LRRK2 at a cluster of heterologous phosphosites is associated to disease. We have previously reported subunits of the PP1 and PP2A classes of phosphatases as well as the PAK6 kinase as regulators of LRRK2 dephosphorylation. We therefore hypothesized that PAK6 may have a functional link with LRRK2's phosphatases. To investigate this, we used PhosTag gel electrophoresis with purified proteins and found that PAK6 phosphorylates the PP2A regulatory subunit PPP2R2C at position S381. While S381 phosphorylation did not affect PP2A holoenzyme formation, a S381A phosphodead PPP2R2C showed impaired binding to LRRK2. Also, PAK6 kinase activity changed PPP2R2C subcellular localization in a S381 phosphorylation-dependent manner. Finally, PAK6-mediated dephosphorylation of LRRK2 was unaffected by phosphorylation of PPP2R2C at S381, suggesting that the previously reported mechanism whereby PAK6-mediated phosphorylation of 14-3-3 proteins promotes 14-3-3-LRRK2 complex dissociation and consequent exposure of LRRK2 phosphosites for dephosphorylation is dominant. Taken together, we conclude that PAK6-mediated phosphorylation of PPP2R2C influences the recruitment of PPP2R2C to the LRRK2 complex and PPP2R2C subcellular localization, pointing to an additional mechanism in the fine-tuning of LRRK2 phosphorylation.
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Affiliation(s)
- Lucia Iannotta
- Department of Biology, University of Padova, Padua, Italy
- National Research Council, c/o Humanitas Research Hospital, Institute of Neuroscience, Rozzano, Italy
| | - Marco Emanuele
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Giulia Favetta
- Department of Biology, University of Padova, Padua, Italy
| | - Giulia Tombesi
- Department of Biology, University of Padova, Padua, Italy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Laurine Vandewynckel
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Jean-Michel Saliou
- University of Lille, CNRS, Inserm, CHU Lille, Institute Pasteur de Lille, US 41 – UAR 2014 – PLBS, Lille, France
| | - Matthieu Drouyer
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - William Sibran
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Laura Civiero
- Department of Biology, University of Padova, Padua, Italy
- IRCSS, San Camillo Hospital, Venice, Italy
| | - R. Jeremy Nichols
- Department of Pathology, Stanford University, Stanford, CA, United States
| | | | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
- YETEM-Innovative Technologies Application and Research Centre, Suleyman Demirel University West Campus, Isparta, Turkey
| | | | - Elisa Greggio
- Department of Biology, University of Padova, Padua, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padua, Italy
| | - Jean-Marc Taymans
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
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5
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Li Z, Weller CA, Shah S, Johnson N, Hao Y, Roberts J, Bereda C, Klaisner S, Machado P, Fratta P, Petrucelli L, Prudencio M, Oskarsson B, Staff NP, Dickson DW, Cookson MR, Ward ME, Singleton AB, Nalls MA, Qi YA. ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571327. [PMID: 38168437 PMCID: PMC10760195 DOI: 10.1101/2023.12.12.571327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe , accompanied by a web interface.
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6
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Guffens L, Derua R, Janssens V. PME-1 sensitizes glioblastoma cells to oxidative stress-induced cell death by attenuating PP2A-B55α-mediated inactivation of MAPKAPK2-RIPK1 signaling. Cell Death Discov 2023; 9:265. [PMID: 37500619 PMCID: PMC10374899 DOI: 10.1038/s41420-023-01572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
Glioblastoma (GBM) is the most common primary brain tumor in adults. Current standard therapy is surgery followed by radiotherapy, with concurrent and adjuvant temozolomide chemotherapy. GBM is characterized by almost uniformly fatal outcomes, highlighting the unmet clinical need for more efficient, biomarker-guided treatments. Protein phosphatase methylesterase-1 (PME-1), a regulator of the tumor suppressive phosphatase PP2A, promotes PP2A demethylation and inactivation, and is overexpressed in 44% of GBM, associated with increased tumor grade and cellular proliferation. Here, we aimed to investigate how reactive oxygen species (ROS), a frequent by-product of radiotherapy and temozolomide chemotherapy, regulate PP2A function via its methylesterase PME-1, and how PME-1 overexpression impacts the response of GBM cells to oxidative stress. We found that in two glioblastoma cell lines, U87MG and U251MG, expression of PME-1 is positively correlated with the sensitivity of the cells to H2O2 or t-BHP-induced oxidative stress. Experiments using the irreversible pharmacologic PME-1 inhibitor, AMZ30, and different PME-1 mutants, revealed that the methylesterase function, the PP2A binding capacity, and the nuclear localization of PME-1 are all important for the sensitizing effect of PME-1 expression. Furthermore, we identified increased nuclear localization of the PP2A-B55α subunit, increased binding of PP2A-B55α to PME-1, and increased B55α-bound PP2A-C demethylation upon oxidative stress. Lastly, we uncovered increased stress-induced phosphorylation and activity of MAPKAPK2 and RIPK1 in PME-1 overexpressing U87MG cells, which caused the observed sensitization to t-BHP treatment. Our data reveal a novel role for PME-1 in oxidative stress-induced GBM cell death, regulating nuclear PP2A-B55α activity and MAPKAPK2-RIPK1 signaling. Patients with GBM tumors overexpressing PME-1, although having a worse prognosis due to increased cellular proliferation of the tumor, could actually be more responsive to oxidative stress-inducing therapies.
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Affiliation(s)
- Liesbeth Guffens
- Laboratory of Protein Phosphorylation & Proteomics, Dept. Cellular & Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
- KU Leuven Cancer Institute (LKI), B-3000, Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation & Proteomics, Dept. Cellular & Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium
- SyBioMa, KU Leuven, B-3000, Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Dept. Cellular & Molecular Medicine, KU Leuven, B-3000, Leuven, Belgium.
- KU Leuven Cancer Institute (LKI), B-3000, Leuven, Belgium.
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7
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Zhong B, An Y, Gao H, Zhao L, Li X, Liang Z, Zhang Y, Zhao Q, Zhang L. In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions. Anal Chim Acta 2023; 1265:341273. [PMID: 37230567 DOI: 10.1016/j.aca.2023.341273] [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: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Comprehensive interactome analysis of targeted proteins is important to understand how proteins work together in regulating functions. Commonly, affinity purification followed by mass spectrometry (AP-MS) has been recognized as the most often used technique for studying protein-protein interactions (PPIs). However, some proteins with weak interactions, which are responsible for key roles in regulation, are easily broken during cell lysis and purification through an AP approach. Herein, we have developed an approach termed in vivo cross-linking-based affinity purification and mass spectrometry (ICAP-MS). By this method, in vivo cross-linking was introduced to covalently fix intracellular PPIs in their functional states to assure all PPIs could be integrally maintained during cell disruption. In addition, the chemically cleavable crosslinkers which were employed enabled unbinding of PPIs for in-depth identification of components within the interactome and biological analysis, while allowing binding of PPIs for cross-linking-mass spectrometry (CXMS)-based direct interaction determination. Multi-level information on targeted PPIs network can be obtained by ICAP-MS, including composition of interacting proteins, as well as direct interacting partners and binding sites. As a proof of concept, the interactome of MAPK3 from 293A cells was profiled with 6.15-fold improvement in identification than by conventional AP-MS. Meanwhile, 184 cross-link site pairs of these PPIs were experimentally identified by CXMS. Furthermore, ICAP-MS was applied in the temporal profiling of MAPK3 interactions under activation by cAMP-mediated pathway. The regulatory manner of MAPK pathways was presented through the quantitative changes of MAPK3 and its interacting proteins at different time points after activation. Therefore, all reported results demonstrated that the ICAP-MS approach may provide comprehensive information on interactome of targeted protein for functional exploration.
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Affiliation(s)
- Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Yuxin An
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
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8
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Zhou Q, Hao B, Cao X, Gao L, Yu Z, Zhao Y, Zhu M, Zhong G, Chi F, Dai X, Mao J, Zhu Y, Rong P, Chen L, Bai X, Ye C, Chen S, Liang T, Li L, Feng XH, Tan M, Zhao B. Energy sensor AMPK gamma regulates translation via phosphatase PPP6C independent of AMPK alpha. Mol Cell 2022; 82:4700-4711.e12. [PMID: 36384136 DOI: 10.1016/j.molcel.2022.10.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/02/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Maintenance of energy level to drive movements and material exchange with the environment is a basic principle of life. AMP-activated protein kinase (AMPK) senses energy level and is a major regulator of cellular energy responses. The gamma subunit of AMPK senses elevated ratio of AMP to ATP and allosterically activates the alpha catalytic subunit to phosphorylate downstream effectors. Here, we report that knockout of AMPKγ, but not AMPKα, suppressed phosphorylation of eukaryotic translation elongation factor 2 (eEF2) induced by energy starvation. We identified PPP6C as an AMPKγ-regulated phosphatase of eEF2. AMP-bound AMPKγ sequesters PPP6C, thereby blocking dephosphorylation of eEF2 and thus inhibiting translation elongation to preserve energy and to promote cell survival. Further phosphoproteomic analysis identified additional targets of PPP6C regulated by energy stress in an AMPKγ-dependent manner. Thus, AMPKγ senses cellular energy availability to regulate not only AMPKα kinase, but also PPP6C phosphatase and possibly other effectors.
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Affiliation(s)
- Qi Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaolei Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Lin Gao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Zhenyue Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Mingrui Zhu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guoxuan Zhong
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Fangtao Chi
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Dai
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jizhong Mao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yibing Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ping Rong
- MOE Key Laboratory of Model Animal for Disease Study and State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Liang Chen
- MOE Key Laboratory of Model Animal for Disease Study and State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Cunqi Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai Chen
- MOE Key Laboratory of Model Animal for Disease Study and State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Li Li
- Institute of Aging Research, Hangzhou Normal University, Hangzhou 311121, China
| | - Xin-Hua Feng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Bin Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Cancer Center, Zhejiang University, Hangzhou 310058, China; Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing 321000, China.
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9
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Protein Phosphatase 2A (PP2A) mutations in brain function, development, and neurologic disease. Biochem Soc Trans 2021; 49:1567-1588. [PMID: 34241636 DOI: 10.1042/bst20201313] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022]
Abstract
By removing Ser/Thr-specific phosphorylations in a multitude of protein substrates in diverse tissues, Protein Phosphatase type 2A (PP2A) enzymes play essential regulatory roles in cellular signalling and physiology, including in brain function and development. Here, we review current knowledge on PP2A gene mutations causally involved in neurodevelopmental disorders and intellectual disability, focusing on PPP2CA, PPP2R1A and PPP2R5D. We provide insights into the impact of these mutations on PP2A structure, substrate specificity and potential function in neurobiology and brain development.
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10
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Abstract
Cancer accounted for 16% of all death worldwide in 2018. Significant progress has been made in understanding tumor occurrence, progression, diagnosis, treatment, and prognosis at the molecular level. However, genomics changes cannot truly reflect the state of protein activity in the body due to the poor correlation between genes and proteins. Quantitative proteomics, capable of quantifying the relatively different protein abundance in cancer patients, has been increasingly adopted in cancer research. Quantitative proteomics has great application potentials, including cancer diagnosis, personalized therapeutic drug selection, real-time therapeutic effects and toxicity evaluation, prognosis and drug resistance evaluation, and new therapeutic target discovery. In this review, the development, testing samples, and detection methods of quantitative proteomics are introduced. The biomarkers identified by quantitative proteomics for clinical diagnosis, prognosis, and drug resistance are reviewed. The challenges and prospects of quantitative proteomics for personalized medicine are also discussed.
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11
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 2020; 184:545-559.e22. [PMID: 33357446 PMCID: PMC7836100 DOI: 10.1016/j.cell.2020.12.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/21/2020] [Accepted: 12/11/2020] [Indexed: 02/02/2023]
Abstract
Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology. Dynamic structural proteomic screens detect functional changes at high resolution Detect enzyme activity, phosphorylation, and molecular interactions in situ Generate new molecular hypotheses and increase functional proteomics coverage Enabled discovery of a regulatory mechanism of glucose uptake in E. coli
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12
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Damacharla D, Thamilselvan V, Zhang X, Mestareehi A, Yi Z, Kowluru A. Quantitative proteomics reveals novel interaction partners of Rac1 in pancreatic β-cells: Evidence for increased interaction with Rac1 under hyperglycemic conditions. Mol Cell Endocrinol 2019; 494:110489. [PMID: 31202817 PMCID: PMC6686664 DOI: 10.1016/j.mce.2019.110489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022]
Abstract
Rac1, a small G protein, regulates physiological insulin secretion from the pancreatic β-cell. Interestingly, Rac1 has also been implicated in the onset of metabolic dysfunction of the β-cell under the duress of hyperglycemia (HG). This study is aimed at the identification of interaction partners of Rac1 in β-cells under basal and HG conditions. Using co-immunoprecipitation and UPLC-ESI-MS/MS, we identified 324 Rac1 interaction partners in INS-1832/13 cells, which represent the largest Rac1 interactome to date. Furthermore, we identified 27 interaction partners that exhibited increased association with Rac1 in β-cells exposed to HG. Western blotting (INS-1832/13 cells, rat islets and human islets) and co-immunoprecipitation (INS-1832/13 cells) further validated the identity of these Rac1 interaction partners including regulators of GPCR-G protein-effector coupling in the islet. These data form the basis for future investigations on contributory roles of these Rac1-specific signaling pathways in islet β-cell function in health and diabetes.
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Affiliation(s)
- Divyasri Damacharla
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA
| | - Vijayalakshmi Thamilselvan
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA
| | - Aktham Mestareehi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA
| | - Anjaneyulu Kowluru
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, USA; Center for Translational Research in Diabetes, Biomedical Research Service, John D. Dingell VA Medical Center, Detroit, MI, 48201, USA.
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13
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Lee IY, Lim JM, Cho H, Kim E, Kim Y, Oh HK, Yang WS, Roh KH, Park HW, Mo JS, Yoon JH, Song HK, Choi EJ. MST1 Negatively Regulates TNFα-Induced NF-κB Signaling through Modulating LUBAC Activity. Mol Cell 2019; 73:1138-1149.e6. [DOI: 10.1016/j.molcel.2019.01.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/20/2018] [Accepted: 01/14/2019] [Indexed: 12/25/2022]
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14
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Elgenaidi IS, Spiers JP. Regulation of the phosphoprotein phosphatase 2A system and its modulation during oxidative stress: A potential therapeutic target? Pharmacol Ther 2019; 198:68-89. [PMID: 30797822 DOI: 10.1016/j.pharmthera.2019.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Phosphoprotein phosphatases are of growing interest in the pathophysiology of many diseases and are often the neglected partner of protein kinases. One family member, PP2A, accounts for dephosphorylation of ~55-70% of all serine/threonine phosphosites. Interestingly, dysregulation of kinase signalling is a hallmark of many diseases in which an increase in oxidative stress is also noted. With this in mind, we assess the evidence to support oxidative stress-mediated regulation of the PP2A system In this article, we first present an overview of the PP2A system before providing an analysis of the regulation of PP2A by endogenous inhibitors, post translational modification, and miRNA. Next, a detailed critique of data implicating reactive oxygen species, ischaemia, ischaemia-reperfusion, and hypoxia in regulating the PP2A holoenzyme and associated regulators is presented. Finally, the pharmacological targeting of PP2A, its endogenous inhibitors, and enzymes responsible for its post-translational modification are covered. There is extensive evidence that oxidative stress modulates multiple components of the PP2A system, however, most of the data pertains to the catalytic subunit of PP2A. Irrespective of the underlying aetiology, free radical-mediated attenuation of PP2A activity is an emerging theme. However, in many instances, a dichotomy exists, which requires clarification and mechanistic insight. Nevertheless, this raises the possibility that pharmacological activation of PP2A, either through small molecule activators of PP2A or CIP2A/SET antagonists may be beneficial in modulating the cellular response to oxidative stress. A better understanding of which, will have wide ranging implications for cancer, heart disease and inflammatory conditions.
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Affiliation(s)
- I S Elgenaidi
- Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland
| | - J P Spiers
- Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland.
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15
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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16
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Edwards SL, Mergan L, Parmar B, Cockx B, De Haes W, Temmerman L, Schoofs L. Exploring neuropeptide signalling through proteomics and peptidomics. Expert Rev Proteomics 2018; 16:131-137. [DOI: 10.1080/14789450.2019.1559733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | - Lucas Mergan
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Bhavesh Parmar
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Bram Cockx
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Wouter De Haes
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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17
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Calderón-Celis F, Encinar JR, Sanz-Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:715-737. [PMID: 28758227 DOI: 10.1002/mas.21542] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and elemental) proteomics is provided in this review.
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Affiliation(s)
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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18
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He X, Sui Y, Wang S. Stepwise frontal affinity chromatography model for drug and protein interaction. Anal Bioanal Chem 2018; 410:5807-5815. [DOI: 10.1007/s00216-018-1194-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 12/12/2022]
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19
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Qian X, Zhao Z, Shang W, Xu Z, Zhang B, Cai H. Serum proteomic analysis of the anti‑arthritic effects of sinomenine on rats with collagen‑induced arthritis. Mol Med Rep 2018; 18:49-58. [PMID: 29749546 PMCID: PMC6059692 DOI: 10.3892/mmr.2018.8959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/16/2018] [Indexed: 12/25/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease, which is characterized by inflammatory synovitis, and the subsequent destruction of articular cartilage and bone. Sinomenine is a traditional Chinese medicine, which has been employed as a clinical treatment for RA for several years in China. The present study investigated the anti‑arthritic effects of sinomenine on Sprague‑Dawley rats with collagen‑induced arthritis (CIA). The differentially expressed proteins in serum were measured by proteomic analysis in order to generate a differentially expressed protein network. A total of 320 differentially expressed proteins were detected in the drug‑treated group compared with in the control group. In the sinomenine‑treated group, 79 differentially expressed proteins were detected compared with in the model group, and among these, 46 proteins were upregulated. Gene ontology analysis revealed that five functions were affected by sinomenine treatment of CIA rats compared with in the model group. In addition, Ingenuity® Pathway Analysis was used to measure enriched signaling pathways, which revealed nuclear factor‑κB, histones, heat shock proteins and protein kinase B as core proteins, generating ~60 pair associations in the network. To the best of our knowledge, the present study is the first to perform proteomic analysis in sinomenine‑treated CIA rats, and the results revealed that numerous targets were involved in the process. In addition, the present study provided a novel approach and evidence for exploring the biological effects of sinomenine. Therefore, the findings of the present study may provide a novel insight into the anti‑RA mechanisms of sinomenine, and may justify further exploration into its function in other relevant diseases.
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Affiliation(s)
- Xin Qian
- Department of Nursing, Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Zhiming Zhao
- Integrated Traditional Chinese and Western Medicine, Nanjing General Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Wei Shang
- Integrated Traditional Chinese and Western Medicine, Nanjing General Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Zhihan Xu
- Department of Nursing, Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Beibei Zhang
- Integrated Traditional Chinese and Western Medicine, Nanjing General Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Hui Cai
- Integrated Traditional Chinese and Western Medicine, Nanjing General Hospital, Nanjing, Jiangsu 210002, P.R. China
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20
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Liu X, Salokas K, Tamene F, Jiu Y, Weldatsadik RG, Öhman T, Varjosalo M. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun 2018; 9:1188. [PMID: 29568061 PMCID: PMC5864832 DOI: 10.1038/s41467-018-03523-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome. AP-MS and BioID provide complementary insights into cellular protein interaction networks. To facilitate their combined use, the authors here present an AP-MS- and BioID-compatible affinity tag, enabling efficient determination of cellular protein locations and interaction distances.
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Affiliation(s)
- Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Rigbe G Weldatsadik
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tiina Öhman
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland. .,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland. .,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland.
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21
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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22
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Abstract
Absolute protein quantification for the analysis of proteome dynamics is more and more required by the scientific community. Therefore a number of methods have recently been reported that aim at determining concentrations of single proteins in complex samples, all of them having their advantages and limitations. However, for all of these methods an accurate and protein unspecific determination of the total protein amount in a given sample is urgently needed. Here a ninhydrin-based assay established to reach this goal is described. Moreover, an optimized protocol for protein digestion is an inevitable prerequisite for all mass spectrometry-based approaches aiming at absolute protein quantification. In this chapter, various aspects are described which have to be considered during validation of a suitable digestion method and a detailed protocol is presented that can be applied to the digestion of soluble proteins originated from microbes.In order to provide an absolute protein quantification workflow applicable for small scale and large scale approaches, a step-by-step guide is provided for the so-called AQUA-strategy (AQUA = absolute quantification), including selection of suited standard peptides, the development of optimized MS methods and the determination of absolute protein concentration using stable isotope dilution and selected reaction monitoring (SID-SRM). Subsequently, a workflow is introduced that combines targeted mass spectrometry and two-dimensional polyacrylamide gel electrophoresis for the large-scale determination of absolute protein amounts.
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Affiliation(s)
- Sandra Maaß
- Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany.
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23
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Creighton MT, Kolton A, Kataya ARA, Maple-Grødem J, Averkina IO, Heidari B, Lillo C. Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors. PLANT, CELL & ENVIRONMENT 2017; 40:2347-2358. [PMID: 28741704 DOI: 10.1111/pce.13038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 05/13/2023]
Abstract
Protein phosphatase 2A catalytic subunit (PP2A-C) has a terminal leucine subjected to methylation, a regulatory mechanism conserved from yeast to mammals and plants. Two enzymes, LCMT1 and PME1, methylate and demethylate PP2A-C, respectively. The physiological importance of these posttranslational modifications is still enigmatic. We investigated these processes in Arabidopsis thaliana by mutant phenotyping, by global expression analysis, and by monitoring methylation status of PP2A-C under different environmental conditions. The lcmt1 mutant, possessing essentially only unmethylated PP2A-C, had less dense rosettes, and earlier flowering than wild type (WT). The pme1 mutant, with 30% reduction in unmethylated PP2A-C, was phenotypically comparable with WT. Approximately 200 overlapping genes were twofold upregulated, and 200 overlapping genes were twofold downregulated in both lcmt1 and pme1 relative to WT. Differences between the 2 mutants were also striking; 97 genes were twofold upregulated in pme1 compared with lcmt1, indicating that PME1 acts as a negative regulator for these genes. Analysis of enriched GO terms revealed categories of both abiotic and biotic stress genes. Furthermore, methylation status of PP2A-C was influenced by environmental stress, especially by hypoxia and salt stress, which led to increased levels of unmethylated PP2A-C, and highlights the importance of PP2A-C methylation/demethylation in environmental responses.
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Affiliation(s)
- Maria T Creighton
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Anna Kolton
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
- Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, 31-425 Kraków, Poland
| | - Amr R A Kataya
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Jodi Maple-Grødem
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Irina O Averkina
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Behzad Heidari
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
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Ishii K, Zhou M, Uchiyama S. Native mass spectrometry for understanding dynamic protein complex. Biochim Biophys Acta Gen Subj 2017; 1862:275-286. [PMID: 28965879 DOI: 10.1016/j.bbagen.2017.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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25
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Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS. G3-GENES GENOMES GENETICS 2017; 7:2249-2258. [PMID: 28522639 PMCID: PMC5499132 DOI: 10.1534/g3.117.042564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Receptor for Activated protein C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for internal ribosome entry site (IRES)-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition (DDA and DIA, respectively) and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method, both in terms of identification of interactants and quantification of low abundance proteins. These data represent the first SWATH spectral library available for Drosophila and will be a useful resource for the community. A total of 52 interacting proteins were identified, including several molecules involved in translation such as structural components of the ribosome, factors regulating translation initiation or elongation, and RNA binding proteins. Among these 52 proteins, 15 were identified as partners by the SWATH strategy only. Interestingly, these 15 proteins are significantly enriched for the functions translation and nucleic acid binding. This enrichment reflects the engagement of RACK1 at the ribosome and highlights the added value of SWATH analysis. A functional screen did not reveal any protein sharing the interesting properties of RACK1, which is required for IRES-dependent translation and not essential for cell viability. Intriguingly however, 10 of the RACK1 partners identified restrict replication of Cricket paralysis virus (CrPV), an IRES-containing virus.
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26
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Min KW, Davila S, Zealy RW, Lloyd LT, Lee IY, Lee R, Roh KH, Jung A, Jemielity J, Choi EJ, Chang JH, Yoon JH. eIF4E phosphorylation by MST1 reduces translation of a subset of mRNAs, but increases lncRNA translation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:761-772. [PMID: 28487214 DOI: 10.1016/j.bbagrm.2017.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Post-transcriptional gene regulation is an important step in eukaryotic gene expression. The last step to govern production of nascent peptides is during the process of mRNA translation. mRNA translation is controlled by many translation initiation factors that are susceptible to post-translational modifications. Here we report that one of the translation initiation factors, eIF4E, is phosphorylated by Mammalian Ste20-like kinase (MST1). Upon phosphorylation, eIF4E weakly interacts with the 5' CAP to inhibit mRNA translation. Simultaneously, active polyribosome is more associated with long noncoding RNAs (lncRNAs). Moreover, the linc00689-derived micropeptide, STORM (Stress- and TNF-α-activated ORF Micropeptide), is triggered by TNF-α-induced and MST1-mediated eIF4E phosphorylation, which exhibits molecular mimicry of SRP19 and, thus, competes for 7SL RNA. Our findings have uncovered a novel function of MST1 in mRNA and lncRNA translation by direct phosphorylation of eIF4E. This novel signaling pathway will provide new platforms for regulation of mRNA translation via post-translational protein modification.
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Affiliation(s)
- Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Richard W Zealy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lawson T Lloyd
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - In Young Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Rumi Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyung Hye Roh
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Ahjin Jung
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Eui-Ju Choi
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA.
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27
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Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell Syst 2017; 4:430-444.e5. [PMID: 28330616 DOI: 10.1016/j.cels.2017.02.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/10/2017] [Accepted: 02/15/2017] [Indexed: 10/19/2022]
Abstract
Coordinated activities of protein kinases and phosphatases ensure phosphorylation homeostasis, which, when perturbed, can instigate diseases, including cancer. Yet, in contrast to kinases, much less is known about protein phosphatase functions and their interactions and complexes. Here, we used quantitative affinity proteomics to assay protein-protein interactions for 54 phosphatases distributed across the three major protein phosphatase families, with additional analysis of their 12 co-factors. We identified 838 high-confidence interactions, of which 631, to our knowledge, have not been reported before. We show that inhibiting the activity of phosphatases PP1 and PP2A by okadaic acid disrupts their specific interactions, supporting the potential of therapeutics that target these proteins. Additional analyses revealed candidate physical and functional interaction links to phosphatase-based regulation of several signaling pathways and to human cancer. Our study provides an initial glimpse of the protein interaction landscape of phosphatases and their functions in cellular regulation.
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Affiliation(s)
- Leena Yadav
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helka Göös
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Riku Katainen
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki 00014, Finland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
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28
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Qin G, Ma J, Chen X, Chu Z, She YM. Methylated-antibody affinity purification to improve proteomic identification of plant RNA polymerase Pol V complex and the interacting proteins. Sci Rep 2017; 7:42943. [PMID: 28224978 PMCID: PMC5320500 DOI: 10.1038/srep42943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C. By this method, the antibody remains intact and does not interfere with the downstream identification of interacting proteins. Non-specific binding proteins were excluded using 14N/15N-metabolic labeling of wild-type and the transgenic plant counterparts. The method was employed to identify 12 co-immunoprecipitated protein subunits in Pol V complex and to discover 17 potential interacting protein targets in Arabidopsis. Our results demonstrated that the modification of antibodies by reductive dimethylation can improve the reliability and sensitivity of identifying low-abundance proteins through on-bead digestion and mass spectrometry. We also show that coupling this technique with chemical crosslinking enables in-depth characterization of endogenous protein complexes and the protein-protein interaction networks including mapping the surface topology and post-translational modifications of interacting proteins.
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Affiliation(s)
- Guochen Qin
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Xiaomei Chen
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center and Shanghai Chenshan Botanic Garden, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China.,Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
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29
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von Stechow L, Olsen JV. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies. Proteomics 2017; 17:1600018. [PMID: 27682984 PMCID: PMC5333460 DOI: 10.1002/pmic.201600018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 12/31/2022]
Abstract
Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways, collectively known as the DNA damage response (DDR). Deciphering DDR signalling pathways with high-throughput technologies could provide insights into oncogenic transformation, metastasis formation and therapy responses, and could build a basis for better therapeutic interventions in cancer treatment. Mass spectrometry (MS)-based proteomics emerged as a method of choice for global studies of proteins and their posttranslational modifications (PTMs). MS-based studies of the DDR have aided in delineating DNA damage-induced signalling responses. Those studies identified changes in abundance, interactions and modification of proteins in the context of genotoxic stress. Here we review ground-breaking MS-based proteomics studies, which analysed changes in protein abundance, protein-protein and protein-DNA interactions, phosphorylation, acetylation, ubiquitylation, SUMOylation and Poly(ADP-ribose)ylation (PARylation) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels.
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Affiliation(s)
- Louise von Stechow
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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30
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Manninen A, Varjosalo M. A proteomics view on integrin-mediated adhesions. Proteomics 2016; 17. [PMID: 27723259 DOI: 10.1002/pmic.201600022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/05/2016] [Accepted: 10/06/2016] [Indexed: 01/15/2023]
Abstract
Individual cells in multicellular organisms constantly explore their microenvironment, or niche, to obtain spatial information that is used to regulate cell behavior to maintain tissue integrity. The extracellular matrix (ECM) is an important source of such spatial information. Binding of the integrin family receptors to the ECM triggers formation of integrin adhesion complexes (IACs) that link the ECM network to cellular cytoskeleton via remarkably large multiprotein complexes collectively referred to as the integrin adhesome. Recent advances in proteomics have enabled researchers to study the IAC composition in detail. Various biochemical IAC isolation methods and culture conditions have been employed to study the composition and dynamics of integrin-mediated adhesions mainly in fibroblasts and lymphoblasts. These studies have led to identification of daunting lists of potential IAC components. This review focuses on the current status of proteomics-driven research seeking to understand integrin functions by comprehensive analysis of IAC components. These systems level approaches have revealed the complexity of biochemical and biomechanical signals that are processed at IACs and provide a novel insight into how these signals are conveyed to regulate cellular behavior.
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Affiliation(s)
- Aki Manninen
- Biocenter Oulu, Oulu Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Biocenter 3, University of Helsinki, Helsinki, Finland
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31
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Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R. Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling. J Proteome Res 2016; 16:14-33. [PMID: 27762135 DOI: 10.1021/acs.jproteome.6b00728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
NF-κB is a family of ubiquitous dimeric transcription factors that play a role in a myriad of cellular processes, ranging from differentiation to stress response and immunity. In inflammation, activation of NF-κB is mediated by pro-inflammatory cytokines, in particular the prototypic cytokines IL-1β and TNF-α, which trigger the activation of complex signaling cascades. In spite of decades of research, the system level understanding of TNF-α signaling is still incomplete. This is partially due to the limited knowledge at the proteome level. The objective of this review is to summarize and critically evaluate the current status of the proteomic research on TNF-α signaling. We will discuss the merits and flaws of the existing studies as well as the insights that they have generated into the proteomic landscape and architecture connected to this signaling pathway. Besides delineating past and current trends in TNF-α proteomic research, we will identify research directions and new methodologies that can further contribute to characterize the TNF-α associated proteome in space and time.
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Affiliation(s)
- Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland
| | - Etienne Caron
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland
| | - Federico Uliana
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich , 8093 Zurich, Switzerland.,Faculty of Science, University of Zurich , 8006 Zurich, Switzerland
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32
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Smits AH, Vermeulen M. Characterizing Protein–Protein Interactions Using Mass Spectrometry: Challenges and Opportunities. Trends Biotechnol 2016; 34:825-834. [DOI: 10.1016/j.tibtech.2016.02.014] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
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33
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Tuncbag N, Gursoy A, Keskin O, Nussinov R. The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Rev Proteomics 2016; 13:447-9. [PMID: 27104235 PMCID: PMC4938151 DOI: 10.1080/14789450.2016.1182023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nurcan Tuncbag
- Middle East Technical University, Graduate School of Informatics, Department of Health Informatics, Ankara, Turkey
| | - Attila Gursoy
- Koc University, Center for Computational Biology and Bioinformatics, Istanbul, Turkey
- Koc University, Computer Engineering, College of Engineering, Istanbul, Turkey
| | - Ozlem Keskin
- Koc University, Center for Computational Biology and Bioinformatics, Istanbul, Turkey
- Koc University, Computer Engineering, College of Engineering, Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, Maryland, United States
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel
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34
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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35
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Zhang X, Damacharla D, Ma D, Qi Y, Tagett R, Draghici S, Kowluru A, Yi Z. Quantitative proteomics reveals novel protein interaction partners of PP2A catalytic subunit in pancreatic β-cells. Mol Cell Endocrinol 2016; 424:1-11. [PMID: 26780722 PMCID: PMC4779412 DOI: 10.1016/j.mce.2016.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/15/2015] [Accepted: 01/07/2016] [Indexed: 12/19/2022]
Abstract
Protein phosphatase 2A (PP2A) is one of the major serine/threonine phosphatases. We hypothesize that PP2A regulates signaling cascades in pancreatic β-cells in the context of glucose-stimulated insulin secretion (GSIS). Using co-immunoprecipitation (co-IP) and tandem mass spectrometry, we globally identified the protein interaction partners of the PP2A catalytic subunit (PP2Ac) in insulin-secreting pancreatic β-cells. Among the 514 identified PP2Ac interaction partners, 476 were novel. This represents the first global view of PP2Ac protein-protein interactions caused by hyperglycemic conditions. Additionally, numerous PP2Ac partners were found involved in a variety of signaling pathways in the β-cell function, such as insulin secretion. Our data suggest that PP2A interacts with various signaling proteins necessary for physiological insulin secretion as well as signaling proteins known to regulate cell dysfunction and apoptosis in the pancreatic β-cells.
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Affiliation(s)
- Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Divyasri Damacharla
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Danjun Ma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Yue Qi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Rebecca Tagett
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI, USA
| | - Anjaneyulu Kowluru
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA; β-Cell Biochemistry Laboratory, John D. Dingell VA Medical Center, Detroit, MI, 48201, USA
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
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36
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Maaß S, Becher D. Methods and applications of absolute protein quantification in microbial systems. J Proteomics 2016; 136:222-33. [PMID: 26825536 DOI: 10.1016/j.jprot.2016.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/05/2016] [Accepted: 01/21/2016] [Indexed: 02/05/2023]
Abstract
In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.
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Affiliation(s)
- Sandra Maaß
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany
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Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 2015; 163:712-23. [PMID: 26496610 DOI: 10.1016/j.cell.2015.09.053] [Citation(s) in RCA: 895] [Impact Index Per Article: 99.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023]
Abstract
The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis.
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Affiliation(s)
- Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nina C Hubner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Ina Weisswange
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Eupheria Biotech GmbH, 01307 Dresden, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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38
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Caruso M, Zhang X, Ma D, Yang Z, Qi Y, Yi Z. Novel Endogenous, Insulin-Stimulated Akt2 Protein Interaction Partners in L6 Myoblasts. PLoS One 2015; 10:e0140255. [PMID: 26465754 PMCID: PMC4605787 DOI: 10.1371/journal.pone.0140255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/23/2015] [Indexed: 12/28/2022] Open
Abstract
Insulin resistance and Type 2 diabetes are marked by an aberrant response in the insulin signaling network. The phosphoinositide-dependent serine/threonine kinase, Akt2, plays a key role in insulin signaling and glucose uptake, most notably within skeletal muscle. Protein-protein interaction regulates the functional consequence of Akt2 and in turn, Akt2's role in glucose uptake. However, only few insulin-responsive Akt2 interaction partners have been identified in skeletal muscle cells. In the present work, rat L6 myoblasts, a widely used insulin sensitive skeletal muscle cell line, were used to examine endogenous, insulin-stimulated Akt2 protein interaction partners. Akt2 co-immunoprecipitation was coupled with 1D-SDS-PAGE and fractions were analyzed by HPLC-ESI-MS/MS to reveal Akt2 protein-protein interactions. The pull-down assay displayed specificity for the Akt2 isoform; Akt1 and Akt3 unique peptides were not detected. A total of 49 were detected with a significantly increased (47) or decreased (2) association with Akt2 following insulin administration (n = 4; p<0.05). Multiple pathways were identified for the novel Akt2 interaction partners, such as the EIF2 and ubiquitination pathways. These data suggest that multiple new endogenous proteins may associate with Akt2 under basal as well as insulin-stimulated conditions, providing further insight into the insulin signaling network. Data are available via ProteomeXchange with identifier PXD002557.
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Affiliation(s)
- Michael Caruso
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Danjun Ma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Zhao Yang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Yue Qi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI, United States of America
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Glatter T, Ahrné E, Schmidt A. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res 2015; 14:4472-85. [PMID: 26412744 DOI: 10.1021/acs.jproteome.5b00654] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.
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Affiliation(s)
- Timo Glatter
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Erik Ahrné
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
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40
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Meyer K, Selbach M. Quantitative affinity purification mass spectrometry: a versatile technology to study protein-protein interactions. Front Genet 2015; 6:237. [PMID: 26236332 PMCID: PMC4500955 DOI: 10.3389/fgene.2015.00237] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/25/2015] [Indexed: 01/11/2023] Open
Abstract
While the genomic revolution has dramatically accelerated the discovery of disease-associated genes, the functional characterization of the corresponding proteins lags behind. Most proteins fulfill their tasks in complexes with other proteins, and analysis of protein–protein interactions (PPIs) can therefore provide insights into protein function. Several methods can be used to generate large-scale protein interaction networks. However, most of these approaches are not quantitative and therefore cannot reveal how perturbations affect the network. Here, we illustrate how a clever combination of quantitative mass spectrometry with different biochemical methods provides a rich toolkit to study different aspects of PPIs including topology, subunit stoichiometry, and dynamic behavior.
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Affiliation(s)
- Katrina Meyer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
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41
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Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods 2015; 12:725-31. [PMID: 26121405 DOI: 10.1038/nmeth.3472] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/06/2015] [Indexed: 01/12/2023]
Abstract
Antibodies are used in multiple cell biology applications, but there are no standardized methods to assess antibody quality-an absence that risks data integrity and reproducibility. We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in immunoprecipitates of 1,124 new recombinant antibodies for 152 chromatin-related human proteins by comparing normalized spectral abundance factors from the target antigen with those of all other proteins. We validated the performance of the standard operating procedure in blinded studies in five independent laboratories. Antibodies for which the target antigen or a member of its known protein complex was the most abundant protein were classified as 'IP gold standard'. This method generates quantitative outputs that can be stored and archived in public databases, and it represents a step toward a platform for community benchmarking of antibody quality.
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42
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Wedeking T, Löchte S, Richter CP, Bhagawati M, Piehler J, You C. Single Cell GFP-Trap Reveals Stoichiometry and Dynamics of Cytosolic Protein Complexes. NANO LETTERS 2015; 15:3610-3615. [PMID: 25901412 DOI: 10.1021/acs.nanolett.5b01153] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We developed in situ single cell pull-down (SiCPull) of GFP-tagged protein complexes based on micropatterned functionalized surface architectures. Cells cultured on these supports are lysed by mild detergents and protein complexes captured to the surface are probed in situ by total internal reflection fluorescence microscopy. Using SiCPull, we quantitatively mapped the lifetimes of various signal transducer and activator of transcription complexes by monitoring dissociation from the surface and defined their stoichiometry on the single molecule level.
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Affiliation(s)
- Tim Wedeking
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | | | - Maniraj Bhagawati
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
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43
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Quantitative interaction proteomics of neurodegenerative disease proteins. Cell Rep 2015; 11:1134-46. [PMID: 25959826 PMCID: PMC9014711 DOI: 10.1016/j.celrep.2015.04.030] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 11/20/2022] Open
Abstract
Several proteins have been linked to neurodegenerative disorders (NDDs), but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP) and Presenilin-1 (PSEN1) for Alzheimer’s disease (AD), Huntingtin (HTT) for Huntington’s disease, Parkin (PARK2) for Parkinson’s disease, and Ataxin-1 (ATXN1) for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early-onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD. Hosp et al. show that quantitative interaction proteomics of neurodegenerative disease proteins captures interactions relevant to pathogenesis. Differential interactome mapping reveals preferential binding of the mitochondrial protein LRPPRC with an early-onset Alzheimer’s disease (AD) variant of APP, potentially contributing to mitochondrial dysfunction observed in AD.
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44
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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45
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Haesen D, Sents W, Lemaire K, Hoorne Y, Janssens V. The Basic Biology of PP2A in Hematologic Cells and Malignancies. Front Oncol 2014; 4:347. [PMID: 25566494 PMCID: PMC4263090 DOI: 10.3389/fonc.2014.00347] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/20/2014] [Indexed: 12/30/2022] Open
Abstract
Reversible protein phosphorylation plays a crucial role in regulating cell signaling. In normal cells, phosphoregulation is tightly controlled by a network of protein kinases counterbalanced by several protein phosphatases. Deregulation of this delicate balance is widely recognized as a central mechanism by which cells escape external and internal self-limiting signals, eventually resulting in malignant transformation. A large fraction of hematologic malignancies is characterized by constitutive or unrestrained activation of oncogenic kinases. This is in part achieved by activating mutations, chromosomal rearrangements, or constitutive activation of upstream kinase regulators, in part by inactivation of their anti-oncogenic phosphatase counterparts. Protein phosphatase 2A (PP2A) represents a large family of cellular serine/threonine phosphatases with suspected tumor suppressive functions. In this review, we highlight our current knowledge about the complex structure and biology of these phosphatases in hematologic cells, thereby providing the rationale behind their diverse signaling functions. Eventually, this basic knowledge is a key to truly understand the tumor suppressive role of PP2A in leukemogenesis and to allow further rational development of therapeutic strategies targeting PP2A.
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Affiliation(s)
- Dorien Haesen
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Ward Sents
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Katleen Lemaire
- Gene Expression Unit, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Yana Hoorne
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
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46
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Lillo C, Kataya ARA, Heidari B, Creighton MT, Nemie-Feyissa D, Ginbot Z, Jonassen EM. Protein phosphatases PP2A, PP4 and PP6: mediators and regulators in development and responses to environmental cues. PLANT, CELL & ENVIRONMENT 2014; 37:2631-48. [PMID: 24810976 DOI: 10.1111/pce.12364] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 05/23/2023]
Abstract
The three closely related groups of serine/threonine protein phosphatases PP2A, PP4 and PP6 are conserved throughout eukaryotes. The catalytic subunits are present in trimeric and dimeric complexes with scaffolding and regulatory subunits that control activity and confer substrate specificity to the protein phosphatases. In Arabidopsis, three scaffolding (A subunits) and 17 regulatory (B subunits) proteins form complexes with five PP2A catalytic subunits giving up to 255 possible combinations. Three SAP-domain proteins act as regulatory subunits of PP6. Based on sequence similarities with proteins in yeast and mammals, two putative PP4 regulatory subunits are recognized in Arabidopsis. Recent breakthroughs have been made concerning the functions of some of the PP2A and PP6 regulatory subunits, for example the FASS/TON2 in regulation of the cellular skeleton, B' subunits in brassinosteroid signalling and SAL proteins in regulation of auxin transport. Reverse genetics is starting to reveal also many more physiological functions of other subunits. A system with key regulatory proteins (TAP46, TIP41, PTPA, LCMT1, PME-1) is present in all eukaryotes to stabilize, activate and inactivate the catalytic subunits. In this review, we present the status of knowledge concerning physiological functions of PP2A, PP4 and PP6 in Arabidopsis, and relate these to yeast and mammals.
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Affiliation(s)
- Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
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47
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Boja ES, Rodriguez H. Proteogenomic convergence for understanding cancer pathways and networks. Clin Proteomics 2014; 11:22. [PMID: 24994965 PMCID: PMC4067069 DOI: 10.1186/1559-0275-11-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
Abstract
During the past several decades, the understanding of cancer at the molecular level has been primarily focused on mechanisms on how signaling molecules transform homeostatically balanced cells into malignant ones within an individual pathway. However, it is becoming more apparent that pathways are dynamic and crosstalk at different control points of the signaling cascades, making the traditional linear signaling models inadequate to interpret complex biological systems. Recent technological advances in high throughput, deep sequencing for the human genomes and proteomic technologies to comprehensively characterize the human proteomes in conjunction with multiplexed targeted proteomic assays to measure panels of proteins involved in biologically relevant pathways have made significant progress in understanding cancer at the molecular level. It is undeniable that proteomic profiling of differentially expressed proteins under many perturbation conditions, or between normal and "diseased" states is important to capture a first glance at the overall proteomic landscape, which has been a main focus of proteomics research during the past 15-20 years. However, the research community is gradually shifting its heavy focus from that initial discovery step to protein target verification using multiplexed quantitative proteomic assays, capable of measuring changes in proteins and their interacting partners, isoforms, and post-translational modifications (PTMs) in response to stimuli in the context of signaling pathways and protein networks. With a critical link to genotypes (i.e., high throughput genomics and transcriptomics data), new and complementary information can be gleaned from multi-dimensional omics data to (1) assess the effect of genomic and transcriptomic aberrations on such complex molecular machinery in the context of cell signaling architectures associated with pathological diseases such as cancer (i.e., from genotype to proteotype to phenotype); and (2) target pathway- and network-driven changes and map the fluctuations of these functional units (proteins) responsible for cellular activities in response to perturbation in a spatiotemporal fashion to better understand cancer biology as a whole system.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, 31 Center Drive, MSC 2580, 20892 Bethesda, MD, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, 31 Center Drive, MSC 2580, 20892 Bethesda, MD, USA
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48
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Caruso M, Ma D, Msallaty Z, Lewis M, Seyoum B, Al-janabi W, Diamond M, Abou-Samra AB, Højlund K, Tagett R, Draghici S, Zhang X, Horowitz JF, Yi Z. Increased interaction with insulin receptor substrate 1, a novel abnormality in insulin resistance and type 2 diabetes. Diabetes 2014; 63:1933-47. [PMID: 24584551 PMCID: PMC4030113 DOI: 10.2337/db13-1872] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Insulin receptor substrate 1 (IRS1) is a key mediator of insulin signal transduction. Perturbations involving IRS1 complexes may lead to the development of insulin resistance and type 2 diabetes (T2D). Surprisingly little is known about the proteins that interact with IRS1 in humans under health and disease conditions. We used a proteomic approach to assess IRS1 interaction partners in skeletal muscle from lean healthy control subjects (LCs), obese insulin-resistant nondiabetic control subjects (OCs), and participants with T2D before and after insulin infusion. We identified 113 novel endogenous IRS1 interaction partners, which represents the largest IRS1 interactome in humans and provides new targets for studies of IRS1 complexes in various diseases. Furthermore, we generated the first global picture of IRS1 interaction partners in LCs, and how they differ in OCs and T2D patients. Interestingly, dozens of proteins in OCs and/or T2D patients exhibited increased associations with IRS1 compared with LCs under the basal and/or insulin-stimulated conditions, revealing multiple new dysfunctional IRS1 pathways in OCs and T2D patients. This novel abnormality, increased interaction of multiple proteins with IRS1 in obesity and T2D in humans, provides new insights into the molecular mechanism of insulin resistance and identifies new targets for T2D drug development.
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Affiliation(s)
- Michael Caruso
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
| | - Danjun Ma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
| | - Zaher Msallaty
- Division of Endocrinology, Wayne State University School of Medicine, Wayne State University, Detroit, MI
| | - Monique Lewis
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
| | - Berhane Seyoum
- Division of Endocrinology, Wayne State University School of Medicine, Wayne State University, Detroit, MI
| | - Wissam Al-janabi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
| | - Michael Diamond
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MIDepartment of Obstetrics and Gynecology, Georgia Regents University, Augusta, GA
| | - Abdul B Abou-Samra
- Division of Endocrinology, Wayne State University School of Medicine, Wayne State University, Detroit, MIDepartment of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Kurt Højlund
- Diabetes Research Centre, Department of Endocrinology, Odense University Hospital, Odense, Denmark
| | - Rebecca Tagett
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI
| | - Sorin Draghici
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
| | | | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, Detroit, MI
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49
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Biopharmaceutical protein production bySaccharomyces cerevisiae: current state and future prospects. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Płociński P, Laubitz D, Cysewski D, Stoduś K, Kowalska K, Dziembowski A. Identification of protein partners in mycobacteria using a single-step affinity purification method. PLoS One 2014; 9:e91380. [PMID: 24664103 PMCID: PMC3963859 DOI: 10.1371/journal.pone.0091380] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/07/2014] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tuberculosis), is thus vital. We have implemented improved screening methods for protein–protein interactions based on affinity purification followed by high-resolution mass spectrometry. This method can be efficiently applied to both medium- and high-throughput studies aiming to characterize protein–protein interaction networks of tubercle bacilli. Of the 4 tested epitopes FLAG, enhanced green fluorescent protein (eGFP), protein A and haemagglutinin, the eGFP tag was found to be most useful on account of its easily monitored expression and its ability to function as a simultaneous tool for subcellular localization studies. It presents a relatively low background with cost-effective purification. RNA polymerase subunit A (RpoA) was used as a model for investigation of a large protein complex. When used as bait, it co-purified with all remaining RNA polymerase core subunits as well as many accessory proteins. The amount of RpoA strongly correlated with the amount of quantification peptide used as part of the tagging system in this study (SH), making it applicable for semi-quantification studies. Interactions between the components of the RpoA-eGFP protein complex were further confirmed using protein cross-linking. Dynamic changes in the composition of protein complexes under induction of UV damage were observed when UvrA-eGFP expressing cells treated with UV light were used to co-purify UvrA interaction partners.
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Affiliation(s)
- Przemysław Płociński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Daniel Laubitz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krystian Stoduś
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Katarzyna Kowalska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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