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Sewell AK, Poss ZC, Ebmeier CC, Jacobsen JR, Old WM, Han M. The TORC1 phosphoproteome in C. elegans reveals roles in transcription and autophagy. iScience 2022; 25:104186. [PMID: 35479415 PMCID: PMC9036118 DOI: 10.1016/j.isci.2022.104186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The protein kinase complex target of rapamycin complex 1 (TORC1) is a critical mediator of nutrient sensing that has been widely studied in cultured cells and yeast, yet our understanding of the regulatory activities of TORC1 in the context of a whole, multi-cellular organism is still very limited. Using Caenorhabditis elegans, we analyzed the DAF-15/Raptor-dependent phosphoproteome by quantitative mass spectrometry and characterized direct kinase targets by in vitro kinase assays. Here, we show new targets of TORC1 that indicate previously unknown regulation of transcription and autophagy. Our results further show that DAF-15/Raptor is differentially expressed during postembryonic development, suggesting a dynamic role for TORC1 signaling throughout the life span. This study provides a comprehensive view of the TORC1 phosphoproteome, reveals more than 100 DAF-15/Raptor-dependent phosphosites that reflect the complex function of TORC1 in a whole, multi-cellular organism, and serves as a rich resource to the field. Detailed, unbiased analysis of the Caenorhabditis elegans TORC1 phosphoproteome Characterization of DAF-15 expression and localization TORC1 direct targets with roles in transcription machinery and autophagy Unique technical approach and datasets provide rich resource to the field
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Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM. The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair. Sci Rep 2019; 9:6539. [PMID: 31024071 PMCID: PMC6483993 DOI: 10.1038/s41598-019-42990-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
The chromosome 21 encoded protein kinase DYRK1A is essential for normal human development. Mutations in DYRK1A underlie a spectrum of human developmental disorders, and increased dosage in trisomy 21 is implicated in Down syndrome related pathologies. DYRK1A regulates a diverse array of cellular processes through physical interactions with substrates and binding partners in various subcellular compartments. Despite recent large-scale protein-protein interaction profiling efforts, DYRK1A interactions specific to different subcellular compartments remain largely unknown, impeding progress toward understanding emerging roles for this kinase. Here, we used immunoaffinity purification and quantitative mass spectrometry to identify nuclear interaction partners of endogenous DYRK1A. This interactome was enriched in DNA damage repair factors, transcriptional elongation factors and E3 ubiquitin ligases. We validated an interaction with RNF169, a factor that promotes homology directed repair upon DNA damage, and found that DYRK1A expression and kinase activity are required for maintenance of 53BP1 expression and subsequent recruitment to DNA damage loci. Further, DYRK1A knock out conferred resistance to ionizing radiation in colony formation assays, suggesting that DYRK1A expression decreases cell survival efficiency in response to DNA damage and points to a tumor suppressive role for this kinase.
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Affiliation(s)
- Steven E Guard
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Zachary C Poss
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Christopher C Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Maria Pagratis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Helen Simpson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA.
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Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, Shair MD, Dowell RD, Old WM, Taatjes DJ. Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics. Cell Rep 2016; 15:436-50. [PMID: 27050516 DOI: 10.1016/j.celrep.2016.03.030] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/08/2016] [Accepted: 03/08/2016] [Indexed: 12/22/2022] Open
Abstract
Cortistatin A (CA) is a highly selective inhibitor of the Mediator kinases CDK8 and CDK19. Using CA, we now report a large-scale identification of Mediator kinase substrates in human cells (HCT116). We identified over 16,000 quantified phosphosites including 78 high-confidence Mediator kinase targets within 64 proteins, including DNA-binding transcription factors and proteins associated with chromatin, DNA repair, and RNA polymerase II. Although RNA-seq data correlated with Mediator kinase targets, the effects of CA on gene expression were limited and distinct from CDK8 or CDK19 knockdown. Quantitative proteome analyses, tracking around 7,000 proteins across six time points (0-24 hr), revealed that CA selectively affected pathways implicated in inflammation, growth, and metabolic regulation. Contrary to expectations, increased turnover of Mediator kinase targets was not generally observed. Collectively, these data support Mediator kinases as regulators of chromatin and RNA polymerase II activity and suggest their roles extend beyond transcription to metabolism and DNA repair.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Christopher C Ebmeier
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Aaron T Odell
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | | | - Thomas Lee
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Henry E Pelish
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew D Shair
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Robin D Dowell
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - William M Old
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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Pelish HE, Liau BB, Nitulescu II, Tangpeerachaikul A, Poss ZC, Da Silva DH, Caruso BT, Arefolov A, Fadeyi O, Christie AL, Du K, Banka D, Schneider EV, Jestel A, Zou G, Si C, Ebmeier CC, Bronson RT, Krivtsov AV, Myers AG, Kohl NE, Kung AL, Armstrong SA, Lemieux ME, Taatjes DJ, Shair MD. Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature 2015; 526:273-276. [PMID: 26416749 PMCID: PMC4641525 DOI: 10.1038/nature14904] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 07/14/2015] [Indexed: 12/11/2022]
Abstract
Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors (TFs), and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling TFs and oncogenes 1, 2. BRD4 and CDK7 are positive regulators of SE-mediated transcription3,4,5. In contrast, negative regulators of SE-associated genes have not been well described. Here we report that Mediator-associated kinases cyclin-dependent kinase 8 (CDK8) and CDK19 restrain increased activation of key SE-associated genes in acute myeloid leukaemia (AML) cells. We determined that the natural product cortistatin A (CA) selectively inhibited Mediator kinases, had antileukaemic activity in vitro and in vivo, and disproportionately induced upregulation of SE-associated genes in CA-sensitive AML cell lines but not in CA-insensitive cell lines. In AML cells, CA upregulated SE-associated genes with tumour suppressor and lineage-controlling functions, including the TFs CEBPA, IRF8, IRF1 and ETV66, 7, 8. The BRD4 inhibitor I-BET151 downregulated these SE-associated genes, yet also has antileukaemic activity. Individually increasing or decreasing expression of these TFs suppressed AML cell growth, providing evidence that leukaemia cells are sensitive to dosage of SE-associated genes. Our results demonstrate that Mediator kinases can negatively regulate SE-associated gene expression in specific cell types and can be pharmacologically targeted as a therapeutic approach to AML.
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Affiliation(s)
- Henry E Pelish
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ioana I Nitulescu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | - Diogo H Da Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Brittany T Caruso
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Arefolov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olugbeminiyi Fadeyi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amanda L Christie
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karrie Du
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Deepti Banka
- Division of Hematology/Oncology, Children's Hospital, Boston, MA 02215, USA
| | - Elisabeth V Schneider
- Proteros Biostructures GmbH, Bunsenstrasse 7a, D-82152 Martinsried, Germany.,Max-Planck-Institut für Biochemie, Am Kloperspitz 18, D-82152 Martinsried, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Bunsenstrasse 7a, D-82152 Martinsried, Germany
| | - Ge Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chong Si
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | | | - Andrei V Krivtsov
- Cancer Biology and Genetics Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nancy E Kohl
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | - Matthew D Shair
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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Bancerek J, Poss ZC, Steinparzer I, Sedlyarov V, Pfaffenwimmer T, Mikulic I, Dölken L, Strobl B, Müller M, Taatjes DJ, Kovarik P. CDK8 kinase phosphorylates transcription factor STAT1 to selectively regulate the interferon response. Immunity 2013; 38:250-62. [PMID: 23352233 PMCID: PMC3580287 DOI: 10.1016/j.immuni.2012.10.017] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022]
Abstract
Gene regulation by cytokine-activated transcription factors of the signal transducer and activator of transcription (STAT) family requires serine phosphorylation within the transactivation domain (TAD). STAT1 and STAT3 TAD phosphorylation occurs upon promoter binding by an unknown kinase. Here, we show that the cyclin-dependent kinase 8 (CDK8) module of the Mediator complex phosphorylated regulatory sites within the TADs of STAT1, STAT3, and STAT5, including S727 within the STAT1 TAD in the interferon (IFN) signaling pathway. We also observed a CDK8 requirement for IFN-γ-inducible antiviral responses. Microarray analyses revealed that CDK8-mediated STAT1 phosphorylation positively or negatively regulated over 40% of IFN-γ-responsive genes, and RNA polymerase II occupancy correlated with gene expression changes. This divergent regulation occurred despite similar CDK8 occupancy at both S727 phosphorylation-dependent and -independent genes. These data identify CDK8 as a key regulator of STAT1 and antiviral responses and suggest a general role for CDK8 in STAT-mediated transcription. As such, CDK8 represents a promising target for therapeutic manipulation of cytokine responses.
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Affiliation(s)
- Joanna Bancerek
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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