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Pham L, Arroum T, Wan J, Pavelich L, Bell J, Morse PT, Lee I, Grossman LI, Sanderson TH, Malek MH, Hüttemann M. Regulation of mitochondrial oxidative phosphorylation through tight control of cytochrome c oxidase in health and disease - Implications for ischemia/reperfusion injury, inflammatory diseases, diabetes, and cancer. Redox Biol 2024; 78:103426. [PMID: 39566165 PMCID: PMC11617887 DOI: 10.1016/j.redox.2024.103426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/04/2024] [Accepted: 11/09/2024] [Indexed: 11/22/2024] Open
Abstract
Mitochondria are essential to cellular function as they generate the majority of cellular ATP, mediated through oxidative phosphorylation, which couples proton pumping of the electron transport chain (ETC) to ATP production. The ETC generates an electrochemical gradient, known as the proton motive force, consisting of the mitochondrial membrane potential (ΔΨm, the major component in mammals) and ΔpH across the inner mitochondrial membrane. Both ATP production and reactive oxygen species (ROS) are linked to ΔΨm, and it has been shown that an imbalance in ΔΨm beyond the physiological optimal intermediate range results in excessive ROS production. The reaction of cytochrome c oxidase (COX) of the ETC with its small electron donor cytochrome c (Cytc) is the proposed rate-limiting step in mammals under physiological conditions. The rate at which this redox reaction occurs controls ΔΨm and thus ATP and ROS production. Multiple mechanisms are in place that regulate this reaction to meet the cell's energy demand and respond to acute stress. COX and Cytc have been shown to be regulated by all three main mechanisms, which we discuss in detail: allosteric regulation, tissue-specific isoforms, and post-translational modifications for which we provide a comprehensive catalog and discussion of their functional role with 55 and 50 identified phosphorylation and acetylation sites on COX, respectively. Disruption of these regulatory mechanisms has been found in several common human diseases, including stroke and myocardial infarction, inflammation including sepsis, and diabetes, where changes in COX or Cytc phosphorylation lead to mitochondrial dysfunction contributing to disease pathophysiology. Identification and subsequent targeting of the underlying signaling pathways holds clear promise for future interventions to improve human health. An example intervention is the recently discovered noninvasive COX-inhibitory infrared light therapy that holds promise to transform the current standard of clinical care in disease conditions where COX regulation has gone awry.
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Affiliation(s)
- Lucynda Pham
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Lauren Pavelich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
| | - Jamie Bell
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Division of Pediatric Critical Care, Children's Hospital of Michigan, Central Michigan University, Detroit, MI, 48201, USA.
| | - Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, 31116, Republic of Korea.
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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Aboulache BL, Hoitsma NM, Luger K. Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange. J Biol Chem 2024; 300:107893. [PMID: 39424143 PMCID: PMC11742319 DOI: 10.1016/j.jbc.2024.107893] [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: 07/12/2024] [Revised: 09/13/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024] Open
Abstract
Maintaining the dynamic structure of chromatin is critical for regulating the cellular processes that require access to the DNA template, such as DNA damage repair, transcription, and replication. Histone chaperones and ATP-dependent chromatin remodeling factors facilitate transitions in chromatin structure by assembling and positioning nucleosomes through a variety of enzymatic activities. SMARCAD1 is a unique chromatin remodeler that combines the ATP-dependent ability to exchange histones, with the chaperone-like activity of nucleosome deposition. We have shown previously that phosphorylated SMARCAD1 exhibits reduced binding to nucleosomes. However, it is unknown how phosphorylation affects SMARCAD1's ability to perform its various enzymatic activities. Here we use mutational analysis, activity assays, and mass spectrometry, to probe SMARCAD1 regulation and to investigate the role of its flexible N-terminal region. We show that phosphorylation affects SMARCAD1 binding to nucleosomes, DNA, and histones H2A-H2B, as well as ATP hydrolysis and histone exchange. Conversely, we report only a marginal effect of phosphorylation for histone H3-H4 binding and nucleosome assembly. In addition, the SMARCAD1 N-terminal region is revealed to be critical for nucleosome assembly and histone exchange. Together, this work examines the intricacies of how phosphorylation governs SMARCAD1 activity and provides insight into its complex regulation and diverse activities.
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Affiliation(s)
- Briana L Aboulache
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Nicole M Hoitsma
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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3
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Ojasalu K, Lieber S, Sokol AM, Nist A, Stiewe T, Bullwinkel I, Finkernagel F, Reinartz S, Müller-Brüsselbach S, Grosse R, Graumann J, Müller R. The lysophosphatidic acid-regulated signal transduction network in ovarian cancer cells and its role in actomyosin dynamics, cell migration and entosis. Theranostics 2023; 13:1921-1948. [PMID: 37064875 PMCID: PMC10091871 DOI: 10.7150/thno.81656] [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: 12/08/2022] [Accepted: 02/25/2023] [Indexed: 04/18/2023] Open
Abstract
Lysophosphatidic acid (LPA) species accumulate in the ascites of ovarian high-grade serous cancer (HGSC) and are associated with short relapse-free survival. LPA is known to support metastatic spread of cancer cells by activating a multitude of signaling pathways via G-protein-coupled receptors of the LPAR family. Systematic unbiased analyses of the LPA-regulated signal transduction network in ovarian cancer cells have, however, not been reported to date. Methods: LPA-induced signaling pathways were identified by phosphoproteomics of both patient-derived and OVCAR8 cells, RNA sequencing, measurements of intracellular Ca2+ and cAMP as well as cell imaging. The function of LPARs and downstream signaling components in migration and entosis were analyzed by selective pharmacological inhibitors and RNA interference. Results: Phosphoproteomic analyses identified > 1100 LPA-regulated sites in > 800 proteins and revealed interconnected LPAR1, ROCK/RAC, PKC/D and ERK pathways to play a prominent role within a comprehensive signaling network. These pathways regulate essential processes, including transcriptional responses, actomyosin dynamics, cell migration and entosis. A critical component of this signaling network is MYPT1, a stimulatory subunit of protein phosphatase 1 (PP1), which in turn is a negative regulator of myosin light chain 2 (MLC2). LPA induces phosphorylation of MYPT1 through ROCK (T853) and PKC/ERK (S507), which is majorly driven by LPAR1. Inhibition of MYPT1, PKC or ERK impedes both LPA-induced cell migration and entosis, while interference with ROCK activity and MLC2 phosphorylation selectively blocks entosis, suggesting that MYPT1 figures in both ROCK/MLC2-dependent and -independent pathways. We finally show a novel pathway governed by LPAR2 and the RAC-GEF DOCK7 to be indispensable for the induction of entosis. Conclusion: We have identified a comprehensive LPA-induced signal transduction network controlling LPA-triggered cytoskeletal changes, cell migration and entosis in HGSC cells. Due to its pivotal role in this network, MYPT1 may represent a promising target for interfering with specific functions of PP1 essential for HGSC progression.
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Affiliation(s)
- Kaire Ojasalu
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Sonja Lieber
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Anna M. Sokol
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Andrea Nist
- Genomics Core Facility, Philipps University, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps University, Marburg, Germany
| | - Imke Bullwinkel
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Florian Finkernagel
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
- Bioinformatics Core Facility, Philipps University, Marburg, Germany
| | - Silke Reinartz
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Sabine Müller-Brüsselbach
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Robert Grosse
- Institut for Experimental and Clinical Pharmacology and Toxicology, Albert-Ludwigs University, Freiburg, Germany
| | - Johannes Graumann
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Institute for Translational Proteomics, Philipps University, Marburg, Germany
| | - Rolf Müller
- Department of Translational Oncology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
- ✉ Corresponding author: Rolf Müller, Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany. . Phone: +49 6421 2866236
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4
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Unni P, Friend J, Weinberg J, Okur V, Hochscherf J, Dominguez I. Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases. Front Mol Biosci 2022; 9:851547. [PMID: 36310603 PMCID: PMC9608649 DOI: 10.3389/fmolb.2022.851547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.
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Affiliation(s)
- Prasida Unni
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Jack Friend
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston University, Boston, MA, United States
| | - Volkan Okur
- New York Genome Center, New York, NY, United States
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
- *Correspondence: Isabel Dominguez,
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5
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Moro L, Simoneschi D, Kurz E, Arbini AA, Jang S, Guaragnella N, Giannattasio S, Wang W, Chen YA, Pires G, Dang A, Hernandez E, Kapur P, Mishra A, Tsirigos A, Miller G, Hsieh JT, Pagano M. Epigenetic silencing of the ubiquitin ligase subunit FBXL7 impairs c-SRC degradation and promotes epithelial-to-mesenchymal transition and metastasis. Nat Cell Biol 2020; 22:1130-1142. [PMID: 32839549 PMCID: PMC7484425 DOI: 10.1038/s41556-020-0560-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic plasticity is a pivotal factor that drives metastasis. Here, we show that the promoter of the gene that encodes the ubiquitin ligase subunit FBXL7 is hypermethylated in advanced prostate and pancreatic cancers, correlating with decreased FBXL7 mRNA and protein levels. Low FBXL7 mRNA levels are predictive of poor survival in patients with pancreatic and prostatic cancers. FBXL7 mediates the ubiquitylation and proteasomal degradation of active c-SRC after its phosphorylation at Ser 104. The DNA-demethylating agent decitabine recovers FBXL7 expression and limits epithelial-to-mesenchymal transition and cell invasion in a c-SRC-dependent manner. In vivo, FBXL7-depleted cancer cells form tumours with a high metastatic burden. Silencing of c-SRC or treatment with the c-SRC inhibitor dasatinib together with FBXL7 depletion prevents metastases. Furthermore, decitabine reduces metastases derived from prostate and pancreatic cancer cells in a FBXL7-dependent manner. Collectively, this research implicates FBXL7 as a metastasis-suppressor gene and suggests therapeutic strategies to counteract metastatic dissemination of pancreatic and prostatic cancer cells.
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Affiliation(s)
- Loredana Moro
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Emma Kurz
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Arnaldo A Arbini
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Shaowen Jang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Wei Wang
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Yu-An Chen
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Geoffrey Pires
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andrew Dang
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth Hernandez
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ankita Mishra
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - George Miller
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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6
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Golkowski M, Vidadala VN, Lau HT, Shoemaker A, Shimizu-Albergine M, Beavo J, Maly DJ, Ong SE. Kinobead/LC-MS Phosphokinome Profiling Enables Rapid Analyses of Kinase-Dependent Cell Signaling Networks. J Proteome Res 2020; 19:1235-1247. [PMID: 32037842 DOI: 10.1021/acs.jproteome.9b00742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Kinase-catalyzed protein phosphorylation is fundamental to eukaryotic signal transduction, regulating most cellular processes. Kinases are frequently dysregulated in cancer, inflammation, and degenerative diseases, and because they can be inhibited with small molecules, they became important drug targets. Accordingly, analytical approaches that determine kinase activation states are critically important to understand kinase-dependent signal transduction and to identify novel drug targets and predictive biomarkers. Multiplexed inhibitor beads (MIBs or kinobeads) efficiently enrich kinases from cell lysates for liquid chromatography-mass spectrometry (LC-MS) analysis. When combined with phosphopeptide enrichment, kinobead/LC-MS can also quantify the phosphorylation state of kinases, which determines their activation state. However, an efficient kinobead/LC-MS kinase phospho-profiling protocol that allows routine analyses of cell lines and tissues has not yet been developed. Here, we present a facile workflow that quantifies the global phosphorylation state of kinases with unprecedented sensitivity. We also found that our kinobead/LC-MS protocol can measure changes in kinase complex composition and show how these changes can indicate kinase activity. We demonstrate the utility of our approach in specifying kinase signaling pathways that control the acute steroidogenic response in Leydig cells; this analysis establishes the first comprehensive framework for the post-translational control of steroid biosynthesis.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | | | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Anna Shoemaker
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Masami Shimizu-Albergine
- University of Washington Medicine Diabetes Institute, University of Washington, Seattle, Washington 98109, United States
| | - Joseph Beavo
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
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7
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Harding RJ, Loppnau P, Ackloo S, Lemak A, Hutchinson A, Hunt B, Holehouse AS, Ho JC, Fan L, Toledo-Sherman L, Seitova A, Arrowsmith CH. Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems. J Biol Chem 2019; 294:6986-7001. [PMID: 30842263 PMCID: PMC6497952 DOI: 10.1074/jbc.ra118.007204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
The gene mutated in individuals with Huntington's disease (HD) encodes the 348-kDa huntingtin (HTT) protein. Pathogenic HD CAG-expansion mutations create a polyglutamine (polyQ) tract at the N terminus of HTT that expands above a critical threshold of ∼35 glutamine residues. The effect of these HD mutations on HTT is not well understood, in part because it is difficult to carry out biochemical, biophysical, and structural studies of this large protein. To facilitate such studies, here we have generated expression constructs for the scalable production of HTT in multiple eukaryotic expression systems. Our set of HTT expression clones comprised both N- and C-terminally FLAG-tagged HTT constructs with polyQ lengths representative of the general population, HD patients, and juvenile HD patients, as well as the more extreme polyQ expansions used in some HD tissue and animal models. Our expression system yielded milligram quantities of pure recombinant HTT protein, including many of the previously mapped post-translational modifications. We characterized both apo and HTT-HTT-associated protein 40 (HAP40) complex samples produced with this HD resource, demonstrating that this toolkit can be used to generate physiologically meaningful HTT complexes. We further demonstrate that these resources can produce sufficient material for protein-intensive experiments, such as small-angle X-ray scattering, providing biochemical insight into full-length HTT protein structure. The work outlined and the tools generated here lay a foundation for further biochemical and structural work on the HTT protein and for studying its functional interactions with other biomolecules.
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Affiliation(s)
- Rachel J Harding
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Suzanne Ackloo
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ashley Hutchinson
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Brittany Hunt
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alex S Holehouse
- the Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130
| | - Jolene C Ho
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Lixin Fan
- the Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core of NCI, National Institutes of Health, Frederick, Maryland 21701, and
| | | | - Alma Seitova
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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8
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Steinberg SF. Post-translational modifications at the ATP-positioning G-loop that regulate protein kinase activity. Pharmacol Res 2018; 135:181-187. [PMID: 30048755 DOI: 10.1016/j.phrs.2018.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/27/2022]
Abstract
Protein kinases are a superfamily of enzymes that control a wide range of cellular functions. These enzymes share a highly conserved catalytic core that folds into a similar bilobar three-dimensional structure. One highly conserved region in the protein kinase core is the glycine-rich loop (or G-loop), a highly flexible loop that is characterized by a consensus GxGxxG sequence. The G-loop points toward the catalytic cleft and functions to bind and position ATP for phosphotransfer. Of note, in many protein kinases, the second and third glycine residues in the G-loop triad flank residues that can be targets for phosphorylation (Ser, Thr, or Tyr) or other post-translational modifications (ubiquitination, acetylation, O-GlcNAcylation, oxidation). There is considerable evidence that cyclin-dependent kinases are held inactive through inhibitory phosphorylation of the conserved Thr/Tyr residues in this position of the G-loop and that dephosphorylation by cellular phosphatases is required for CDK activation and progression through the cell cycle. This review summarizes literature that identifies residues in or adjacent to the G-loop in other protein kinases that are targets for functionally important post-translational modifications.
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Affiliation(s)
- Susan F Steinberg
- Department of Pharmacology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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9
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Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal 2016; 9:rs12. [PMID: 27811184 DOI: 10.1126/scisignal.aaf5011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Patients with lung cancers harboring anaplastic lymphoma kinase (ALK) gene fusions benefit from treatment with ALK inhibitors, but acquired resistance inevitably arises. A better understanding of proximal ALK signaling mechanisms may identify sensitizers to ALK inhibitors that disrupt the balance between prosurvival and proapoptotic effector signals. Using affinity purification coupled with mass spectrometry in an ALK fusion lung cancer cell line (H3122), we generated an ALK signaling network and investigated signaling activity using tyrosine phosphoproteomics. We identified a network of 464 proteins composed of subnetworks with differential response to ALK inhibitors. A small hairpin RNA screen targeting 407 proteins in this network revealed 64 and 9 proteins that when knocked down sensitized cells to crizotinib and alectinib, respectively. Among these, knocking down fibroblast growth factor receptor substrate 2 (FRS2) or coiled-coil and C2 domain-containing protein 1A (CC2D1A), both scaffolding proteins, sensitized multiple ALK fusion cell lines to the ALK inhibitors crizotinib and alectinib. Collectively, our data set provides a resource that enhances our understanding of signaling and drug resistance networks consequent to ALK fusions and identifies potential targets to improve the efficacy of ALK inhibitors in patients.
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Affiliation(s)
- Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Hannah Scarborough
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jihye Kim
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrii I Rozhok
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yian Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xiaohui Zhang
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lanxi Song
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Yun Bai
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Richard Z Liu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John Koomen
- Department of Molecular Oncology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Aik Choon Tan
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James Degregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
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10
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Zhang Y, Stefanovic B. Akt mediated phosphorylation of LARP6; critical step in biosynthesis of type I collagen. Sci Rep 2016; 6:22597. [PMID: 26932461 PMCID: PMC4773855 DOI: 10.1038/srep22597] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/17/2016] [Indexed: 12/31/2022] Open
Abstract
La ribonucleoprotein domain family, member 6 (LARP6) is the RNA binding protein, which regulates translation of collagen mRNAs and synthesis of type I collagen. Posttranslational modifications of LARP6 and how they affect type I collagen synthesis have not been studied. We show that in lung fibroblasts LARP6 is phosphorylated at 8 serines, 6 of which are located within C-terminal domain. Phosphorylation of LARP6 follows a hierarchical order; S451 phosphorylation being a prerequisite for phosphorylations of other serines. Inhibition of PI3K/Akt pathway reduced the phosphorylation of LARP6, but had no effect on the S451A mutant, suggesting that PI3K/Akt pathway targets S451 and we have identified Akt as the responsible kinase. Overexpression of S451A mutant had dominant negative effect on collagen biosynthesis; drastically reduced secretion of collagen and induced hyper-modifications of collagen α2 (I) polypeptides. This indicates that LARP6 phosphorylation at S451 is critical for regulating translation and folding of collagen polypeptides. Akt inhibitor, GSK-2141795, which is in clinical trials for treatment of solid tumors, reduced collagen production by human lung fibroblasts with EC50 of 150 nM. This effect can be explained by inhibition of LARP6 phosphorylation and suggests that Akt inhibitors may be effective in treatment of various forms of fibrosis.
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Affiliation(s)
- Yujie Zhang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
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11
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Leitner NR, Witalisz-Siepracka A, Strobl B, Müller M. Tyrosine kinase 2 - Surveillant of tumours and bona fide oncogene. Cytokine 2015; 89:209-218. [PMID: 26631911 DOI: 10.1016/j.cyto.2015.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 10/29/2015] [Indexed: 12/16/2022]
Abstract
Tyrosine kinase 2 (TYK2) is a member of the Janus kinase (JAK) family, which transduces cytokine and growth factor signalling. Analysis of TYK2 loss-of-function revealed its important role in immunity to infection, (auto-) immunity and (auto-) inflammation. TYK2-deficient patients unravelled high similarity between mice and men with respect to cellular signalling functions and basic immunology. Genome-wide association studies link TYK2 to several autoimmune and inflammatory diseases as well as carcinogenesis. Due to its cytokine signalling functions TYK2 was found to be essential in tumour surveillance. Lately TYK2 activating mutants and fusion proteins were detected in patients diagnosed with leukaemic diseases suggesting that TYK2 is a potent oncogene. Here we review the cell intrinsic and extrinsic functions of TYK2 in the characteristics preventing and enabling carcinogenesis. In addition we describe an unexpected function of kinase-inactive TYK2 in tumour rejection.
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Affiliation(s)
- Nicole R Leitner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Agnieszka Witalisz-Siepracka
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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12
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Abstract
During the past 20 years, autophagy signaling has entered the main stage of the cell biological theater. Autophagy represents an intracellular degradation process that is involved in both the bulk recycling of cytoplasmic components and the selective removal of organelles, protein aggregates, or intracellular pathogens. The understanding of autophagy has been greatly facilitated by the characterization of the molecular machinery governing this process. In yeast, initiation of autophagy is controlled by the Atg1 kinase complex, which is composed of the Ser/Thr kinase Atg1, the adaptor protein Atg13, and the ternary complex of Atg17-Atg31-Atg29. In vertebrates, the orthologous ULK1 kinase complex contains the Ser/Thr kinase ULK1 and the accessory proteins ATG13, RB1CC1, and ATG101. Among these components, Atg1/ULK1 have gained major attention in the past, i.e., for the identification of upstream regulatory kinases, the characterization of downstream substrates controlling the autophagic flux, or as a druggable target for the modulation of autophagy. However, accumulating data indicate that the function of Atg13/ATG13 has been likely underestimated so far. In addition to ensuring proper Atg1/ULK1 recruitment and activity, this adaptor molecule has been implicated in ULK1-independent autophagy processes. Furthermore, recent data have identified additional binding partners of Atg13/ATG13 besides the components of the Atg1/ULK1 complex, e.g., Atg8 family proteins or acidic phospholipids. Therefore, in this review we will center the spotlight on Atg13/ATG13 and summarize the role that Atg13/ATG13 assumes in the autophagy stage play.
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Affiliation(s)
- Sebastian Alers
- Institute of Molecular Medicine; Heinrich-Heine-University; Düsseldorf, Germany
| | | | - Björn Stork
- Institute of Molecular Medicine; Heinrich-Heine-University; Düsseldorf, Germany
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13
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Lecat S, Matthes HWD, Pepperkok R, Simpson JC, Galzi JL. A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways. Mol Cell Proteomics 2015; 14:1385-99. [PMID: 25759509 PMCID: PMC4424407 DOI: 10.1074/mcp.m114.046698] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic proteins was performed using translocation criteria. The screening of 193 fluorescently tagged human proteins identified eight proteins that responded to activation of the tachykinin NK2 receptor by a change in their intracellular localization. Previously we have presented the functional characterization of one of these proteins, REDD1, that translocates to the plasma membrane. Here we report the results of the entire screening. The process of cell activation was recorded on videos at different time points and all the videos can be visualized on a dedicated website. The proteins BAIAP3 and BIN1, partially translocated to the plasma membrane upon activation of NK2 receptors. Proteins ARHGAP12 and PKM2 translocated toward membrane blebs. Three proteins that associate with the cytoskeleton were of particular interest : PLEKHH2 rearranged from individual dots located near the cell-substrate adhesion surface into lines of dots. The speriolin-like protein, SPATC1L, redistributed to cell-cell junctions. The Chloride intracellular Channel protein, CLIC2, translocated from actin-enriched plasma membrane bundles to cell-cell junctions upon activation of NK2 receptors. CLIC2, and one of its close paralogs, CLIC4, were further shown to respond with the same translocation pattern to muscarinic M3 and lysophosphatidic LPA receptors. This screen allowed us to identify potential actors in signaling pathways downstream of G protein-coupled receptors and could be scaled-up for high-content screening.
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Affiliation(s)
- Sandra Lecat
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France;
| | - Hans W D Matthes
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France
| | - Rainer Pepperkok
- §European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Jeremy C Simpson
- ¶¶School of Biology and Environmental Science and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jean-Luc Galzi
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France
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14
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Lecat S, Belemnaba L, Galzi JL, Bucher B. Neuropeptide Y receptor mediates activation of ERK1/2 via transactivation of the IGF receptor. Cell Signal 2015; 27:1297-304. [PMID: 25817573 DOI: 10.1016/j.cellsig.2015.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/19/2015] [Accepted: 03/08/2015] [Indexed: 12/24/2022]
Abstract
Neuropeptide Y binds to G-protein coupled receptors whose action results in inhibition of adenylyl cyclase activity. Using HEK293 cells stably expressing the native neuropeptide Y Y1 receptors, we found that the NPY agonist elicits a transient phosphorylation of the extracellular signal-regulated kinases (ERK1/2). We first show that ERK1/2 activation following Y1 receptor stimulation is dependent on heterotrimeric Gi/o since it is completely inhibited by pre-treatment with pertussis toxin. In addition, ERK1/2 activation is internalization-independent since mutant Y1 receptors unable to recruit β-arrestins, can still activate ERK signaling to the same extent as wild-type receptors. We next show that this activation of the MAPK pathway is inhibited by the MEK inhibitor U0126, is not dependent on calcium signaling at the Y1 receptor (no effect upon inhibition of phospholipase C, protein kinase C or protein kinase D) but instead dependent on Gβ/γ and associated signaling pathways that activate PI3-kinase. Although inhibition of the epidermal-growth factor receptor tyrosine kinase did not influence NPY-induced ERK1/2 activation, we show that the inhibition of insulin growth factor receptor IGFR by AG1024 completely blocks activation of ERK1/2 by the Y1 receptor. This Gβ/γ-PI3K-AG1024-sensitive pathway does not involve activation of IGFR through the release of a soluble ligand by metalloproteinases since it is not affected by the metalloproteinase inhibitor marimastat. Finally, we found that a similar pathway, sensitive to wortmannin-AG1024 but insensitive to marimastat, is implicated in activation of ERK signaling in HEK293 cells by endogenously expressed GPCRs coupled to Gq-protein (muscarinic M3 receptors) or coupled to Gs-protein (endothelin ETB receptors). Our analysis is the first to show that β-arrestin recruitment to the NPY Y1 receptor is not necessary for MAPK activation by this receptor but that transactivation of the IGFR receptor is required.
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Affiliation(s)
- Sandra Lecat
- GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis 300 Bvd Sébastien Brant, CS 10413, 67412 Illkirch, France.
| | - Lazare Belemnaba
- UMR 7213, CNRS-University of Strasbourg, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du Rhin, CS 60024, 67401 Illkirch, France
| | - Jean-Luc Galzi
- GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis 300 Bvd Sébastien Brant, CS 10413, 67412 Illkirch, France
| | - Bernard Bucher
- UMR 7213, CNRS-University of Strasbourg, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du Rhin, CS 60024, 67401 Illkirch, France
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15
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Wiese H, Gelis L, Wiese S, Reichenbach C, Jovancevic N, Osterloh M, Meyer HE, Neuhaus EM, Hatt HH, Radziwill G, Warscheid B. Quantitative phosphoproteomics reveals the protein tyrosine kinase Pyk2 as a central effector of olfactory receptor signaling in prostate cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:632-40. [PMID: 25219547 DOI: 10.1016/j.bbapap.2014.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/21/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
Abstract
The prostate-specific G-protein-coupled receptor 1 (PSGR1) is an olfactory receptor specifically expressed in the prostate gland. PSGR1 expression is elevated both in benign prostatic hyperplasia tissue and in prostate cancer. Stimulation of PSGR1 by the odorant β-ionone leads to an increase in the intracellular Ca(2+) concentration, activation of mitogen-activated protein (MAP) kinases and a decrease in prostate cancer cell proliferation. To further extend our knowledge about PSGR1 signaling in prostate cancer cells, we performed a quantitative phosphoproteomics study using stable isotope labeling by amino acids in cell culture and mass spectrometry. We report 51 differentially regulated phosphorylation sites in 24 proteins with functions in cytoskeletal remodeling, signaling and ion transport. Activation of PSGR1 evoked an increase in intracellular pH mediated by the sodium/hydrogen exchanger NHE1. Furthermore, we report the protein tyrosine kinase Pyk2 as a central effector of PSGR1 signaling cascades in LNCaP cells. Our data show that phosphorylation of p38 MAP kinase is triggered by Pyk2. In addition, we confirmed dephosphorylation of the tumor suppressor protein N-myc downstream regulated gene 1 (NDRG1) at Ser330 downstream of Pyk2. Since NDRG1 impacts oncogenic signaling pathways interfering with tumor progression, we suggest that the Pyk2-NDRG1 axis is possibly involved in conveying the anti-proliferative effect of β-ionone in prostate cancer cells. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Heike Wiese
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Lian Gelis
- Department of Cell Physiology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Sebastian Wiese
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Christa Reichenbach
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Nikolina Jovancevic
- Department of Cell Physiology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Markus Osterloh
- Department of Cell Physiology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Helmut E Meyer
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Eva M Neuhaus
- Department of Pharmacology and Toxicology, University of Jena, Drackendorfer Str. 1, 07747 Jena, Germany
| | - Hanns H Hatt
- Department of Cell Physiology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Gerald Radziwill
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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16
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Cui Z, Scruggs SB, Gilda JE, Ping P, Gomes AV. Regulation of cardiac proteasomes by ubiquitination, SUMOylation, and beyond. J Mol Cell Cardiol 2014; 71:32-42. [PMID: 24140722 PMCID: PMC3990655 DOI: 10.1016/j.yjmcc.2013.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/21/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the major intracellular degradation system, and its proper function is critical to the health and function of cardiac cells. Alterations in cardiac proteasomes have been linked to several pathological phenotypes, including cardiomyopathies, ischemia-reperfusion injury, heart failure, and hypertrophy. Defects in proteasome-dependent cellular protein homeostasis can be causal for the initiation and progression of certain cardiovascular diseases. Emerging evidence suggests that the UPS can specifically target proteins that govern pathological signaling pathways for degradation, thus altering downstream effectors and disease outcomes. Alterations in UPS-substrate interactions in disease occur, in part, due to direct modifications of 19S, 11S or 20S proteasome subunits. Post-translational modifications (PTMs) are one facet of this proteasomal regulation, with over 400 known phosphorylation sites, over 500 ubiquitination sites and 83 internal lysine acetylation sites, as well as multiple sites for caspase cleavage, glycosylation (such as O-GlcNAc modification), methylation, nitrosylation, oxidation, and SUMOylation. Changes in cardiac proteasome PTMs, which occur in ischemia and cardiomyopathies, are associated with changes in proteasome activity and proteasome assembly; however several features of this regulation remain to be explored. In this review, we focus on how some of the less common PTMs affect proteasome function and alter cellular protein homeostasis. This article is part of a Special Issue entitled "Protein Quality Control, the Ubiquitin Proteasome System, and Autophagy".
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Affiliation(s)
- Ziyou Cui
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA
| | - Sarah B Scruggs
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
| | - Jennifer E Gilda
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA
| | - Peipei Ping
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA; Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA.
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17
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Knippschild U, Krüger M, Richter J, Xu P, García-Reyes B, Peifer C, Halekotte J, Bakulev V, Bischof J. The CK1 Family: Contribution to Cellular Stress Response and Its Role in Carcinogenesis. Front Oncol 2014; 4:96. [PMID: 24904820 PMCID: PMC4032983 DOI: 10.3389/fonc.2014.00096] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022] Open
Abstract
Members of the highly conserved and ubiquitously expressed pleiotropic CK1 family play major regulatory roles in many cellular processes including DNA-processing and repair, proliferation, cytoskeleton dynamics, vesicular trafficking, apoptosis, and cell differentiation. As a consequence of cellular stress conditions, interaction of CK1 with the mitotic spindle is manifold increased pointing to regulatory functions at the mitotic checkpoint. Furthermore, CK1 is able to alter the activity of key proteins in signal transduction and signal integration molecules. In line with this notion, CK1 is tightly connected to the regulation and degradation of β-catenin, p53, and MDM2. Considering the importance of CK1 for accurate cell division and regulation of tumor suppressor functions, it is not surprising that mutations and alterations in the expression and/or activity of CK1 isoforms are often detected in various tumor entities including cancer of the kidney, choriocarcinomas, breast carcinomas, oral cancer, adenocarcinomas of the pancreas, and ovarian cancer. Therefore, scientific effort has enormously increased (i) to understand the regulation of CK1 and its involvement in tumorigenesis- and tumor progression-related signal transduction pathways and (ii) to develop CK1-specific inhibitors for the use in personalized therapy concepts. In this review, we summarize the current knowledge regarding CK1 regulation, function, and interaction with cellular proteins playing central roles in cellular stress-responses and carcinogenesis.
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Affiliation(s)
- Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
| | - Marc Krüger
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
| | - Julia Richter
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
| | - Pengfei Xu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
| | - Balbina García-Reyes
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
| | - Christian Peifer
- Institute for Pharmaceutical Chemistry, Christian Albrechts University , Kiel , Germany
| | - Jakob Halekotte
- Institute for Pharmaceutical Chemistry, Christian Albrechts University , Kiel , Germany
| | - Vasiliy Bakulev
- Department of Organic Synthesis, Ural Federal University , Ekaterinburg , Russia
| | - Joachim Bischof
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital , Ulm , Germany
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18
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Zhang L, Holmes IP, Hochgräfe F, Walker SR, Ali NA, Humphrey ES, Wu J, de Silva M, Kersten WJA, Connor T, Falk H, Allan L, Street IP, Bentley JD, Pilling PA, Monahan BJ, Peat TS, Daly RJ. Characterization of the novel broad-spectrum kinase inhibitor CTx-0294885 as an affinity reagent for mass spectrometry-based kinome profiling. J Proteome Res 2013; 12:3104-16. [PMID: 23692254 DOI: 10.1021/pr3008495] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Kinase enrichment utilizing broad-spectrum kinase inhibitors enables the identification of large proportions of the expressed kinome by mass spectrometry. However, the existing inhibitors are still inadequate in covering the entire kinome. Here, we identified a novel bisanilino pyrimidine, CTx-0294885, exhibiting inhibitory activity against a broad range of kinases in vitro, and further developed it into a Sepharose-supported kinase capture reagent. Use of a quantitative proteomics approach confirmed the selectivity of CTx-0294885-bound beads for kinase enrichment. Large-scale CTx-0294885-based affinity purification followed by LC-MS/MS led to the identification of 235 protein kinases from MDA-MB-231 cells, including all members of the AKT family that had not been previously detected by other broad-spectrum kinase inhibitors. Addition of CTx-0294885 to a mixture of three kinase inhibitors commonly used for kinase-enrichment increased the number of kinase identifications to 261, representing the largest kinome coverage from a single cell line reported to date. Coupling phosphopeptide enrichment with affinity purification using the four inhibitors enabled the identification of 799 high-confidence phosphosites on 183 kinases, ∼10% of which were localized to the activation loop, and included previously unreported phosphosites on BMP2K, MELK, HIPK2, and PRKDC. Therefore, CTx-0294885 represents a powerful new reagent for analysis of kinome signaling networks that may facilitate development of targeted therapeutic strategies. Proteomics data have been deposited to the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository with the data set identifier PXD000239.
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Affiliation(s)
- Luxi Zhang
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, New South Wales 2010, Australia
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19
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Chang YC, Tang HW, Liang SY, Pu TH, Meng TC, Khoo KH, Chen GC. Evaluation of Drosophila Metabolic Labeling Strategies for in Vivo Quantitative Proteomic Analyses with Applications to Early Pupa Formation and Amino Acid Starvation. J Proteome Res 2013; 12:2138-50. [DOI: 10.1021/pr301168x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ying-Che Chang
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
- Clinical Proteomics
Center, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Hong-Wen Tang
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Suh-Yuen Liang
- NRPB
Core Facilities for Protein
Structural Analysis, Academia Sinica, Taipei,
Taiwan
| | - Tsung-Hsien Pu
- NRPB
Core Facilities for Protein
Structural Analysis, Academia Sinica, Taipei,
Taiwan
| | - Tzu-Ching Meng
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Kay-Hooi Khoo
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Guang-Chao Chen
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
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20
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Mäusbacher N, Schreiber TB, Machatti M, Schaab C, Daub H. Proteome-wide analysis of temporal phosphorylation dynamics in lysophosphatidic acid-induced signaling. Proteomics 2012; 12:3485-98. [PMID: 23090842 DOI: 10.1002/pmic.201200172] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/10/2012] [Accepted: 10/02/2012] [Indexed: 12/14/2022]
Abstract
Most growth factor receptors trigger phosphorylation-based signal transduction to translate environmental stimuli into defined biological responses. In addition to comprehensive and reliable assessment of growth factor-induced phosphoregulation, temporal resolution is needed to gain insights into the organizing principles of the cellular signaling machinery. Here, we introduce a refined experimental design for MS-based phosphoproteomics to reconcile the need for high comprehensiveness and temporal resolution with the key requirement of monitoring biological reproducibility. We treated SILAC-labeled SCC-9 cells with the seven transmembrane receptor ligand lysophosphatidic acid (LPA) and identified more than 17 000 phosphorylation sites. Filtering for biological replicate quantification yielded five-time point profiles for 6292 site-specific phosphorylations, which we analyzed for statistically significant regulation. Notably, about 30% of these sites changed significantly upon LPA stimulation, indicating extensive phosphoproteome regulation in response to this growth factor. Analysis of time series data identified distinct temporal profiles for different kinase substrate motifs, likely reflecting temporal orchestration of cellular kinase activities. Our data further indicated coordinated regulation of biological processes and phosphoprotein networks upon LPA stimulation. Finally, we detected regulation of functionally characterized phosphorylation sites not yet implicated in LPA signaling, which may foster a better understanding how LPA regulates cellular physiology on the molecular level.
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Affiliation(s)
- Nina Mäusbacher
- Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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21
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Rigbolt KTG, Blagoev B. Quantitative phosphoproteomics to characterize signaling networks. Semin Cell Dev Biol 2012; 23:863-71. [PMID: 22677334 DOI: 10.1016/j.semcdb.2012.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/29/2012] [Indexed: 11/20/2022]
Abstract
Reversible protein phosphorylation is involved in the regulation of most, if not all, major cellular processes via dynamic signal transduction pathways. During the last decade quantitative phosphoproteomics have evolved from a highly specialized area to a powerful and versatile platform for analyzing protein phosphorylation at a system-wide scale and has become the intuitive strategy for comprehensive characterization of signaling networks. Contemporary phosphoproteomics use highly optimized procedures for sample preparation, mass spectrometry and data analysis algorithms to identify and quantify thousands of phosphorylations, thus providing extensive overviews of the cellular signaling networks. As a result of these developments quantitative phosphoproteomics have been applied to study processes as diverse as immunology, stem cell biology and DNA damage. Here we review the developments in phosphoproteomics technology that have facilitated the application of phosphoproteomics to signaling networks and introduce examples of recent system-wide applications of quantitative phosphoproteomics. Despite the great advances in phosphoproteomics technology there are still several outstanding issues and we provide here our outlook on the current limitations and challenges in the field.
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Affiliation(s)
- Kristoffer T G Rigbolt
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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22
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Park SS, Wu WW, Zhou Y, Shen RF, Martin B, Maudsley S. Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC). J Proteomics 2012; 75:3720-32. [PMID: 22575385 DOI: 10.1016/j.jprot.2012.04.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/29/2012] [Accepted: 04/24/2012] [Indexed: 12/22/2022]
Abstract
Accurate and reliable quantitative proteomics in cell culture has been considerably facilitated by the introduction of the stable isotope labeling by amino acids in cell culture (SILAC), combined with high resolution mass spectrometry. There are however several major sources of quantification errors that commonly occur with SILAC techniques, i.e. incomplete incorporation of isotopic amino acids, arginine-to-proline conversion, and experimental errors in final sample mixing. Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios. Here we demonstrate that a label-swap replication of SILAC experiments was able to effectively correct experimental errors by averaging ratios measured in individual replicates using quantitative proteomics and phosphoproteomics of ligand treatment of neural cell cultures. Furthermore, this strategy was successfully applied to a SILAC triplet experiment, which presents a much more complicated experimental matrix, affected by both incomplete labeling and arginine-to-proline conversion. Based on our results, we suggest that SILAC experiments should be designed to incorporate label-swap replications for enhanced reliability in expression ratios.
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Affiliation(s)
- Sung-Soo Park
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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23
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Schreiber TB, Mäusbacher N, Soroka J, Wandinger SK, Buchner J, Daub H. Global Analysis of Phosphoproteome Regulation by the Ser/Thr Phosphatase Ppt1 in Saccharomyces cerevisiae. J Proteome Res 2012; 11:2397-408. [DOI: 10.1021/pr201134p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Thiemo B. Schreiber
- Department of Molecular
Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nina Mäusbacher
- Department of Molecular
Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Joanna Soroka
- Center for Integrated Protein Science, Department
of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Sebastian K. Wandinger
- Center for Integrated Protein Science, Department
of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science, Department
of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Henrik Daub
- Department of Molecular
Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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24
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Goel R, Harsha HC, Pandey A, Keshava Prasad TS. Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. MOLECULAR BIOSYSTEMS 2012; 8:453-63. [PMID: 22159132 PMCID: PMC3804167 DOI: 10.1039/c1mb05340j] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.
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Affiliation(s)
- Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, 577 451, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
- Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, India
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25
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Hoffert JD, Pisitkun T, Saeed F, Song JH, Chou CL, Knepper MA. Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics. Mol Cell Proteomics 2011; 11:M111.014613. [PMID: 22108457 DOI: 10.1074/mcp.m111.014613] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate diverse physiological processes, and many human diseases are due to defects in GPCR signaling. To identify the dynamic response of a signaling network downstream from a prototypical G(s)-coupled GPCR, the vasopressin V2 receptor, we have carried out multireplicate, quantitative phosphoproteomics with iTRAQ labeling at four time points following vasopressin exposure at a physiological concentration in cells isolated from rat kidney. A total of 12,167 phosphopeptides were identified from 2,783 proteins, with 273 changing significantly in abundance with vasopressin. Two-dimensional clustering of phosphopeptide time courses and Gene Ontology terms revealed that ligand binding to the V2 receptor affects more than simply the canonical cyclic adenosine monophosphate-protein kinase A and arrestin pathways under physiological conditions. The regulated proteins included key components of actin cytoskeleton remodeling, cell-cell adhesion, mitogen-activated protein kinase signaling, Wnt/β-catenin signaling, and apoptosis pathways. These data suggest that vasopressin can regulate an array of cellular functions well beyond its classical role in regulating water and solute transport. These results greatly expand the current view of GPCR signaling in a physiological context and shed new light on potential roles for this signaling network in disorders such as polycystic kidney disease. Finally, we provide an online resource of physiologically regulated phosphorylation sites with dynamic quantitative data (http://helixweb.nih.gov/ESBL/Database/TiPD/index.html).
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Affiliation(s)
- Jason D Hoffert
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, Mizuno K, Ma'ayan A, Gygi SP, Lefkowitz RJ. Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proc Natl Acad Sci U S A 2010; 107:15299-304. [PMID: 20686112 PMCID: PMC2930550 DOI: 10.1073/pnas.1008461107] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
beta-Arrestin-mediated signaling downstream of seven transmembrane receptors (7TMRs) is a relatively new paradigm for signaling by these receptors. We examined changes in protein phosphorylation occurring when HEK293 cells expressing the angiotensin II type 1A receptor (AT1aR) were stimulated with the beta-arrestin-biased ligand Sar(1), Ile(4), Ile(8)-angiotensin (SII), a ligand previously found to signal through beta-arrestin-dependent, G protein-independent mechanisms. Using a phospho-antibody array containing 46 antibodies against signaling molecules, we found that phosphorylation of 35 proteins increased upon SII stimulation. These SII-mediated phosphorylation events were abrogated after depletion of beta-arrestin 2 through siRNA-mediated knockdown. We also performed an MS-based quantitative phosphoproteome analysis after SII stimulation using a strategy of stable isotope labeling of amino acids in cell culture (SILAC). We identified 1,555 phosphoproteins (4,552 unique phosphopeptides), of which 171 proteins (222 phosphopeptides) showed increased phosphorylation, and 53 (66 phosphopeptides) showed decreased phosphorylation upon SII stimulation of the AT1aR. This study identified 38 protein kinases and three phosphatases whose phosphorylation status changed upon SII treatment. Using computational approaches, we performed system-based analyses examining the beta-arrestin-mediated phosphoproteome including construction of a kinase-substrate network for beta-arrestin-mediated AT1aR signaling. Our analysis demonstrates that beta-arrestin-dependent signaling processes are more diverse than previously appreciated. Notably, our analysis identifies an AT1aR-mediated cytoskeletal reorganization network whereby beta-arrestin regulates phosphorylation of several key proteins, including cofilin and slingshot. This study provides a system-based view of beta-arrestin-mediated phosphorylation events downstream of a 7TMR and opens avenues for research in a rapidly evolving area of 7TMR signaling.
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Affiliation(s)
| | | | | | | | - Bo Zhai
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115
| | - Judit Villén
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115
| | - Wilhelm Haas
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115
| | | | | | | | - Marylens Hernandez
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY 10029; and
| | - Alexander Lachmann
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY 10029; and
| | - Shan Zhao
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY 10029; and
| | | | | | - Kensaku Mizuno
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY 10029; and
| | - Steven P. Gygi
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115
| | - Robert J. Lefkowitz
- Departments of Medicine and
- Biochemistry and
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710
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27
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Mäusbacher N, Schreiber TB, Daub H. Glycoprotein capture and quantitative phosphoproteomics indicate coordinated regulation of cell migration upon lysophosphatidic acid stimulation. Mol Cell Proteomics 2010; 9:2337-53. [PMID: 20639409 DOI: 10.1074/mcp.m110.000737] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The lipid mediator lysophosphatidic acid (LPA) is a serum component that regulates cellular functions such as proliferation, migration, and survival via specific G protein-coupled receptors. The underlying signaling mechanisms are still incompletely understood, including those that operate at the plasma membrane to modulate cell-cell and cell-matrix interactions in LPA-promoted cell migration. To explore LPA-evoked phosphoregulation with a focus on cell surface proteins, we combined glycoproteome enrichment by immobilized lectins with SILAC-based quantitative phosphoproteomics. We performed biological replicate analyses in SCC-9 squamous cell carcinoma cells and repeatedly quantified the effect of 1.5- and 5-min LPA treatment on more than 700 distinct phosphorylations in lectin-purified proteins. We detected many regulated phosphorylation events on various types of plasma membrane proteins such as cell adhesion molecules constituting adherens junctions, desmosomes, and hemidesmosomes. Several of these LPA-regulated phosphorylation sites have been characterized in a biological context other than G protein-coupled receptor signaling, and the transfer of this functional information suggests coordinated and multifactorial cell adhesion control in LPA-induced cell migration. Additionally, we identified LPA-mediated activation loop phosphorylation of the serine/threonine kinase Wnk1 and verified a role of Wnk1 for LPA-induced cell migration in knock-down experiments. In conclusion, the glycoproteome phosphoproteomics strategy described here sheds light on incompletely understood mechanisms in LPA-induced cell migratory behavior.
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Affiliation(s)
- Nina Mäusbacher
- Project Group Cell Signaling, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
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