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Ibáñez-Molero S, Pruijs JTM, Atmopawiro A, Wang F, Terry AM, Altelaar M, Peeper DS, Stecker KE. Phosphoprotein dynamics of interacting T cells and tumor cells by HySic. Cell Rep 2024; 43:113598. [PMID: 38150364 DOI: 10.1016/j.celrep.2023.113598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/16/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Functional interactions between cytotoxic T cells and tumor cells are central to anti-cancer immunity. However, our understanding of the proteins involved is limited. Here, we present HySic (hybrid quantification of stable isotope labeling by amino acids in cell culture [SILAC]-labeled interacting cells) as a method to quantify protein and phosphorylation dynamics between and within physically interacting cells. Using co-cultured T cells and tumor cells, we directly measure the proteome and phosphoproteome of engaged cells without the need for physical separation. We identify proteins whose abundance or activation status changes upon T cell:tumor cell interaction and validate our method with established signal transduction pathways including interferon γ (IFNγ) and tumor necrosis factor (TNF). Furthermore, we identify the RHO/RAC/PAK1 signaling pathway to be activated upon cell engagement and show that pharmacologic inhibition of PAK1 sensitizes tumor cells to T cell killing. Thus, HySic is a simple method to study rapid protein signaling dynamics in physically interacting cells that is easily extended to other biological systems.
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Affiliation(s)
- Sofía Ibáñez-Molero
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Joannes T M Pruijs
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Alisha Atmopawiro
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fujia Wang
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandra M Terry
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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Debets DO, Stecker KE, Piskopou A, Liefaard MC, Wesseling J, Sonke GS, Lips EH, Altelaar M. Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2 + breast cancer. Cell Rep Med 2023; 4:101203. [PMID: 37794585 PMCID: PMC10591042 DOI: 10.1016/j.xcrm.2023.101203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Patients with early-stage HER2-overexpressing breast cancer struggle with treatment resistance in 20%-40% of cases. More information is needed to predict HER2 therapy response and resistance in vivo. In this study, we perform (phospho)proteomics analysis of pre-treatment HER2+ needle biopsies of early-stage invasive breast cancer to identify molecular signatures predictive of treatment response to trastuzumab, pertuzumab, and chemotherapy. Our data show that accurate quantification of the estrogen receptor (ER) and HER2 biomarkers, combined with the assessment of associated biological features, has the potential to enable better treatment outcome prediction. In addition, we identify cellular mechanisms that potentially precondition tumors to resist therapy. We find proteins with expression changes that correlate with resistance and constitute to a strong predictive signature for treatment success in our patient cohort. Our results highlight the multifactorial nature of drug resistance in vivo and demonstrate the necessity of deep tumor profiling.
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Affiliation(s)
- Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Anastasia Piskopou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Marte C Liefaard
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, University of Amsterdam, Amsterdam, the Netherlands
| | - Esther H Lips
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands.
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Wang F, Veth T, Kuipers M, Altelaar M, Stecker KE. Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation. Anal Chem 2023; 95:9471-9479. [PMID: 37319171 PMCID: PMC10308333 DOI: 10.1021/acs.analchem.3c00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. Suspension trapping (S-Trap) is a novel, rapid, and universal method of sample preparation that is increasingly applied in bottom-up proteomics studies. However, the performance of the S-Trap protocol for phosphoproteomics studies is unclear. In the existing S-Trap protocol, the addition of phosphoric acid (PA) and methanol buffer creates a fine protein suspension to capture proteins on a filter and is a critical step for subsequent protein digestion. Herein, we demonstrate that this addition of PA is detrimental to downstream phosphopeptide enrichment, rendering the standard S-Trap protocol suboptimal for phosphoproteomics. In this study, the performance of the S-Trap digestion for proteomics and phosphoproteomics is systematically evaluated in large-scale and small-scale samples. The results of this comparative analysis show that an optimized S-Trap approach, where trifluoroacetic acid is substituted for PA, is a simple and effective method to prepare samples for phosphoproteomics. Our optimized S-Trap protocol is applied to extracellular vesicles to demonstrate superior sample preparation workflow for low-abundance, membrane-rich samples.
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Affiliation(s)
- Fujia Wang
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Tim Veth
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marije Kuipers
- Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584
CM Utrecht, the Netherlands
| | - Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Kelly E. Stecker
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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4
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van den Berg CM, Volkov VA, Schnorrenberg S, Huang Z, Stecker KE, Grigoriev I, Gilani S, Frikstad KAM, Patzke S, Zimmermann T, Dogterom M, Akhmanova A. CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side. J Cell Biol 2023; 222:213861. [PMID: 36752787 PMCID: PMC9948759 DOI: 10.1083/jcb.202208062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/14/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling the formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates the elongation and stability of ciliary axonemes and other microtubule-based structures.
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Affiliation(s)
- Cyntha M. van den Berg
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Vladimir A. Volkov
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands,https://ror.org/02e2c7k09Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Ziqiang Huang
- EMBL Imaging Centre, EMBL-Heidelberg, Heidelberg, Germany
| | - Kelly E. Stecker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Ilya Grigoriev
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Sania Gilani
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Department of Molecular Cell Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kari-Anne M. Frikstad
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sebastian Patzke
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Marileen Dogterom
- https://ror.org/02e2c7k09Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Anna Akhmanova
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands,Correspondence to Anna Akhmanova:
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5
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Vredevoogd DW, Kuilman T, Ligtenberg MA, Boshuizen J, Stecker KE, de Bruijn B, Krijgsman O, Huang X, Kenski JCN, Lacroix R, Mezzadra R, Gomez-Eerland R, Yildiz M, Dagidir I, Apriamashvili G, Zandhuis N, van der Noort V, Visser NL, Blank CU, Altelaar M, Schumacher TN, Peeper DS. Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold. Cell 2020; 180:404-405. [PMID: 31978349 DOI: 10.1016/j.cell.2020.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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6
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Vredevoogd DW, Kuilman T, Ligtenberg MA, Boshuizen J, Stecker KE, de Bruijn B, Krijgsman O, Huang X, Kenski JCN, Lacroix R, Mezzadra R, Gomez-Eerland R, Yildiz M, Dagidir I, Apriamashvili G, Zandhuis N, van der Noort V, Visser NL, Blank CU, Altelaar M, Schumacher TN, Peeper DS. Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold. Cell 2019; 178:585-599.e15. [PMID: 31303383 DOI: 10.1016/j.cell.2019.06.014] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/23/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
New opportunities are needed to increase immune checkpoint blockade (ICB) benefit. Whereas the interferon (IFN)γ pathway harbors both ICB resistance factors and therapeutic opportunities, this has not been systematically investigated for IFNγ-independent signaling routes. A genome-wide CRISPR/Cas9 screen to sensitize IFNγ receptor-deficient tumor cells to CD8 T cell elimination uncovered several hits mapping to the tumor necrosis factor (TNF) pathway. Clinically, we show that TNF antitumor activity is only limited in tumors at baseline and in ICB non-responders, correlating with its low abundance. Taking advantage of the genetic screen, we demonstrate that ablation of the top hit, TRAF2, lowers the TNF cytotoxicity threshold in tumors by redirecting TNF signaling to favor RIPK1-dependent apoptosis. TRAF2 loss greatly enhanced the therapeutic potential of pharmacologic inhibition of its interaction partner cIAP, another screen hit, thereby cooperating with ICB. Our results suggest that selective reduction of the TNF cytotoxicity threshold increases the susceptibility of tumors to immunotherapy.
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Affiliation(s)
- David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Xinyao Huang
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Juliana C N Kenski
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Ruben Lacroix
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Riccardo Mezzadra
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Raquel Gomez-Eerland
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Mete Yildiz
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Ilknur Dagidir
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Nordin Zandhuis
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Vincent van der Noort
- Division of Statistics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Christian U Blank
- Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
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Volkening JD, Stecker KE, Sussman MR. Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana. Mol Cell Proteomics 2019; 18:308-319. [PMID: 30401684 PMCID: PMC6356070 DOI: 10.1074/mcp.ra118.001124] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Indexed: 12/16/2022] Open
Abstract
Modern tandem MS-based sequencing technologies allow for the parallel measurement of concentration and covalent modifications for proteins within a complex sample. Recently, this capability has been extended to probe a proteome's three-dimensional structure and conformational state by determining the thermal denaturation profile of thousands of proteins simultaneously. Although many animals and their resident microbes exist under a relatively narrow, regulated physiological temperature range, plants take on the often widely ranging temperature of their surroundings, possibly influencing the evolution of protein thermal stability. In this report we present the first in-depth look at the thermal proteome of a plant species, the model organism Arabidopsis thaliana By profiling the melting curves of over 1700 Arabidopsis proteins using six biological replicates, we have observed significant correlation between protein thermostability and several known protein characteristics, including molecular weight and the composition ratio of charged to polar amino acids. We also report on a divergence of the thermostability of the core and regulatory domains of the plant 26S proteasome that may reflect a unique property of the way protein turnover is regulated during temperature stress. Lastly, the highly replicated database of Arabidopsis melting temperatures reported herein provides baseline data on the variability of protein behavior in the assay. Unfolding behavior and experiment-to-experiment variability were observed to be protein-specific traits, and thus this data can serve to inform the design and interpretation of future targeted assays to probe the conformational status of proteins from plants exposed to different chemical, environmental and genetic challenges.
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Affiliation(s)
- Jeremy D Volkening
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Utrecht, Netherlands
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706;.
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Minkoff BB, Stecker KE, Sussman MR. Rapid Phosphoproteomic Effects of Abscisic Acid (ABA) on Wild-Type and ABA Receptor-Deficient A. thaliana Mutants. Mol Cell Proteomics 2015; 14:1169-82. [PMID: 25693798 DOI: 10.1074/mcp.m114.043307] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 11/06/2022] Open
Abstract
Abscisic acid (ABA)¹ is a plant hormone that controls many aspects of plant growth, including seed germination, stomatal aperture size, and cellular drought response. ABA interacts with a unique family of 14 receptor proteins. This interaction leads to the activation of a family of protein kinases, SnRK2s, which in turn phosphorylate substrates involved in many cellular processes. The family of receptors appears functionally redundant. To observe a measurable phenotype, four of the fourteen receptors have to be mutated to create a multilocus loss-of-function quadruple receptor (QR) mutant, which is much less sensitive to ABA than wild-type (WT) plants. Given these phenotypes, we asked whether or not a difference in ABA response between the WT and QR backgrounds would manifest on a phosphorylation level as well. We tested WT and QR mutant ABA response using isotope-assisted quantitative phosphoproteomics to determine what ABA-induced phosphorylation changes occur in WT plants within 5 min of ABA treatment and how that phosphorylation pattern is altered in the QR mutant. We found multiple ABA-induced phosphorylation changes that occur within 5 min of treatment, including three SnRK2 autophosphorylation events and phosphorylation on SnRK2 substrates. The majority of robust ABA-dependent phosphorylation changes observed were partially diminished in the QR mutant, whereas many smaller ABA-dependent phosphorylation changes observed in the WT were not responsive to ABA in the mutant. A single phosphorylation event was increased in response to ABA treatment in both the WT and QR mutant. A portion of the discovery data was validated using selected reaction monitoring-based targeted measurements on a triple quadrupole mass spectrometer. These data suggest that different subsets of phosphorylation events depend upon different subsets of the ABA receptor family to occur. Altogether, these data expand our understanding of the model by which the family of ABA receptors directs rapid phosphoproteomic changes.
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Affiliation(s)
- Benjamin B Minkoff
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin, 53706
| | - Kelly E Stecker
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin, 53706
| | - Michael R Sussman
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin, 53706
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9
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Stecker KE, Minkoff BB, Sussman MR. Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response. Plant Physiol 2014; 165:1171-1187. [PMID: 24808101 PMCID: PMC4081330 DOI: 10.1104/pp.114.238816] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/29/2014] [Indexed: 05/18/2023]
Abstract
Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using 15N metabolic labeling and untargeted mass spectrometry with a high-resolution ion-trap instrument. The results from these discovery experiments were then validated using targeted Selected Reaction Monitoring mass spectrometry with a triple quadrupole. Targeted Selected Reaction Monitoring experiments were conducted with plants treated under nine different environmental perturbations to determine whether the phosphorylation changes were specific for osmosignaling or involved cross talk with other signaling pathways. The results indicate that regulatory proteins such as members of the mitogen-activated protein kinase family are specifically phosphorylated in response to osmotic stress. Proteins involved in 5' messenger RNA decapping and phosphatidylinositol 3,5-bisphosphate synthesis were also identified as targets of dehydration-induced phosphoregulation. The results of these experiments demonstrate the utility of targeted phosphoproteomic analysis in understanding protein regulation networks and provide new insight into cellular processes involved in the osmotic stress response.
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Affiliation(s)
- Kelly E Stecker
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Benjamin B Minkoff
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael R Sussman
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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