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Chong L, Hsu CC, Zhu Y. Advances in mass spectrometry-based phosphoproteomics for elucidating abscisic acid signaling and plant responses to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6547-6557. [PMID: 35959917 DOI: 10.1093/jxb/erac324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses have significant impacts on crop yield and quality. Even though significant efforts during the past decade have been devoted to uncovering the core signaling pathways associated with the phytohormone abscisic acid (ABA) and abiotic stress in plants, abiotic stress signaling mechanisms in most crops remain largely unclear. The core components of the ABA signaling pathway, including early events in the osmotic stress-induced phosphorylation network, have recently been elucidated in Arabidopsis with the aid of phosphoproteomics technologies. We now know that SNF1-related kinases 2 (SnRK2s) are not only inhibited by the clade A type 2C protein phosphatases (PP2Cs) through dephosphorylation, but also phosphorylated and activated by upstream mitogen-activated protein kinase kinase kinases (MAP3Ks). Through describing the course of studies to elucidate abiotic stress and ABA signaling, we will discuss how we can take advantage of the latest innovations in mass-spectrometry-based phosphoproteomics and structural proteomics to boost our investigation of plant regulation and responses to ABA and abiotic stress.
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Affiliation(s)
- Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, Hainan, China
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2
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Zhu P, Wu X, Zhang RY, Hsu CC, Zhang ZY, Tao WA. An Integrated Proteomic Strategy to Identify SHP2 Substrates. J Proteome Res 2022; 21:2515-2525. [PMID: 36103635 PMCID: PMC9597472 DOI: 10.1021/acs.jproteome.2c00481] [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] [Indexed: 11/29/2022]
Abstract
Protein phosphatases play an essential role in normal cell physiology and the development of diseases such as cancer. The innate challenges associated with studying protein phosphatases have limited our understanding of their substrates, molecular mechanisms, and unique functions within highly coordinated networks. Here, we introduce a novel strategy using substrate-trapping mutants coupled with quantitative proteomics methods to identify physiological substrates of Src homology 2 containing protein tyrosine phosphatase 2 (SHP2) in a high-throughput manner. The technique integrates three parallel mass spectrometry-based proteomics experiments, including affinity isolation of substrate-trapping mutant complex using wild-type and SHP2 KO cells, in vivo global quantitative phosphoproteomics, and in vitro phosphatase reaction. We confidently identified 18 direct substrates of SHP2 in the epidermal growth factor receptor signaling pathways, including both known and novel SHP2 substrates. Docking protein 1 was further validated using biochemical assays as a novel SHP2 substrate, providing a mechanism for SHP2-mediated Ras activation. This advanced workflow improves the systemic identification of direct substrates of protein phosphatases, facilitating our understanding of the equally important roles of protein phosphatases in cellular signaling.
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Affiliation(s)
- Peipei Zhu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - W Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Karamafrooz A, Brennan J, Thomas DD, Parker LL. Integrated Phosphoproteomics for Identifying Substrates of Human Protein Kinase A ( PRKACA) and Its Oncogenic Mutant DNAJB1 -PRKACA. J Proteome Res 2021; 20:4815-4830. [PMID: 34436901 PMCID: PMC10153428 DOI: 10.1021/acs.jproteome.1c00500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The DNAJB1-PRKACA fusion is the signature genetic event of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare but lethal liver cancer that primarily affects adolescents and young adults. A deletion fuses the first exon of the HSP40 gene (DNAJB1), with exons 2-10 of protein kinase A (PRKACA), producing the chimeric kinase DNAJB1-PKAca (J-PKAca). The HSP40 portion's scaffolding/chaperone function has been implicated in redirecting substrate recognition to upregulate oncogenic pathways, but the direct substrates of this fusion are not fully known. We integrated cell-based and in vitro phosphoproteomics to identify substrates targeted directly by PKA and J-PKAca, comparing phosphoproteome profiles from cells with in vitro rephosphorylation of peptides and proteins from lysates using recombinant enzymes. We identified a subset of phosphorylation sites in both cell-based and in vitro experiments, as well as altered pathways and proteins consistent with observations from related studies. We also treated cells with PKA inhibitors that function by two different mechanisms (rpcAMPs and PKI) and examined phosphoproteome profiles, finding some substrates that persisted in the presence of inhibitors and revealing differences between WT and chimera. Overall, these results provide potential insights into J-PKAca's oncogenic activity in a complex cellular system and may provide candidate targets for therapeutic follow-up.
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Affiliation(s)
- Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Current affiliation: Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Jack Brennan
- Independent Technology Consultant, LIC, Boston, Massachusetts 02129, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Hu Z, Sankar DS, Vu B, Leytens A, Vionnet C, Wu W, Stumpe M, Martínez-Martínez E, Stork B, Dengjel J. ULK1 phosphorylation of striatin activates protein phosphatase 2A and autophagy. Cell Rep 2021; 36:109762. [PMID: 34592149 DOI: 10.1016/j.celrep.2021.109762] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 01/18/2023] Open
Abstract
The evolutionarily conserved ULK1 kinase complex acts as gatekeeper of canonical autophagy and regulates induction of autophagosome biogenesis. To better understand control of ULK1 and analyze whether ULK1 has broader functions that are also linked to the later steps of autophagy, we perform comprehensive phosphoproteomic analyses. Combining in vivo with in vitro data, we identify numerous direct ULK1 target sites within autophagy-relevant proteins that are critical for autophagosome maturation and turnover. In addition, we highlight an intimate crosstalk between ULK1 and several phosphatase complexes. ULK1 is not only a PP2A target but also directly phosphorylates the regulatory PP2A subunit striatin, activating PP2A and serving as positive feedback to promote autophagy-dependent protein turnover. Thus, ULK1 and phosphatase activities are tightly coordinated to robustly regulate protein degradation by autophagy.
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Affiliation(s)
- Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Bich Vu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christine Vionnet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Wenxian Wu
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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Niinae T, Imami K, Sugiyama N, Ishihama Y. Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs. Mol Cell Proteomics 2021; 20:100119. [PMID: 34186244 PMCID: PMC8325102 DOI: 10.1016/j.mcpro.2021.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass-spectrometry-based phosphoproteomics can identify more than 10,000 phosphorylated sites in a single experiment. But, despite the fact that enormous phosphosite information has been accumulated in public repositories, protein kinase–substrate relationships remain largely unknown. Here, we describe a method to identify endogenous substrates of kinases by using a combination of a proximity-dependent biotin identification method, called BioID, with two other independent methods, kinase-perturbed phosphoproteomics and phosphorylation motif matching. For proof of concept, this approach was applied to casein kinase 2 (CK2) and protein kinase A (PKA), and we identified 24 and 35 putative substrates, respectively. We also show that known cancer-associated missense mutations near phosphosites of substrates affect phosphorylation by CK2 or PKA and thus might alter downstream signaling in cancer cells bearing these mutations. This approach extends our ability to probe physiological kinase–substrate networks by providing new methodology for large-scale identification of endogenous substrates of kinases. Identification of novel kinase interactors by BioID. Applying two orthogonal filters, kinase perturbation and phosphorylation motif. Identification of novel CK2 and PKA substrates. A universal method for the identification of endogenous substrates for all kinases.
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Affiliation(s)
- Tomoya Niinae
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; PRESTO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Naoyuki Sugiyama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.
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Sugiyama N. Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. ACTA ACUST UNITED AC 2020; 9:A0082. [PMID: 32547896 PMCID: PMC7242781 DOI: 10.5702/massspectrometry.a0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation mediated by protein kinases is one of the most significant posttranslational modifications in many biological events. The function and physiological substrates of specific protein kinases, which are highly associated with known signal transduction elements or therapeutic targets, have been extensively studied using various approaches; however, most protein kinases have not yet been characterized. In recent decades, many techniques have been developed for the identification of in vitro and physiological substrates of protein kinases. In this review, I summarize recent studies profiling the characteristics of kinases using mass spectrometry-based proteomics, focusing on the large-scale identification of in vitro substrates of the human kinome using a quantitative phosphoproteomics approach.
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Affiliation(s)
- Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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