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Broadus MR, Lee E. Chemical Screening Using Cell-Free Xenopus Egg Extract. Cold Spring Harb Protoc 2018; 2018:pdb.prot098277. [PMID: 29475996 DOI: 10.1101/pdb.prot098277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Most drug screening methods use purified proteins, cultured cells, and/or small model organisms such as Xenopus, zebrafish, flies, or nematodes. These systems have proven successes in drug discovery, but they also have weaknesses. Although purified cellular components allow for identification of compounds with activity against specific targets, such systems lack the complex biological interactions present in cellular and organismal screens. In vivo systems overcome these weaknesses, but the lack of cellular permeability, efflux by cellular pumps, and/or toxicity can be major limitations. Xenopus laevis egg extract, a concentrated and biologically active cytosol, can potentially overcome these weaknesses. Drug interactions occur in a near-physiological milieu, thereby functioning in a "truer" endogenous manner than purified components. Also, Xenopus egg extract is a cell-free system that lacks intact plasma membranes that could restrict drug access to potential targets. Finally, Xenopus egg extract is readily manipulated at the protein level: Proteins are easily depleted or added to the system, an important feature for analyzing drug effects in disease states. Thus, Xenopus egg extract offers an attractive media for screening drugs that merges strengths of both in vitro and in vivo systems.
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Affiliation(s)
- Matthew R Broadus
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt Ingram Cancer Center, Vanderbilt, University Medical Center, Nashville, Tennessee 37232
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Neitzel LR, Broadus MR, Zhang N, Sawyer L, Wallace HA, Merkle JA, Jodoin JN, Sitaram P, Crispi EE, Rork W, Lee LA, Pan D, Gould KL, Page-McCaw A, Lee E. Characterization of a cdc14 null allele in Drosophila melanogaster. Biol Open 2018; 7:bio.035394. [PMID: 29945873 PMCID: PMC6078348 DOI: 10.1242/bio.035394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cdc14 is an evolutionarily conserved serine/threonine phosphatase. Originally identified in Saccharomyces cerevisiae as a cell cycle regulator, its role in other eukaryotic organisms remains unclear. In Drosophila melanogaster, Cdc14 is encoded by a single gene, thus facilitating its study. We found that Cdc14 expression is highest in the testis of adult flies and that cdc14 null flies are viable. cdc14 null female and male flies do not display altered fertility. cdc14 null males, however, exhibit decreased sperm competitiveness. Previous studies have shown that Cdc14 plays a role in ciliogenesis during zebrafish development. In Drosophila, sensory neurons are ciliated. We found that the Drosophila cdc14 null mutants have defects in chemosensation and mechanosensation as indicated by decreased avoidance of repellant substances and decreased response to touch. In addition, we show that cdc14 null mutants have defects in lipid metabolism and resistance to starvation. These studies highlight the diversity of Cdc14 function in eukaryotes despite its structural conservation. Summary: The Cdc14 phosphatase has been implicated in cell cycle regulation in S. cerevisiae. We show that Drosophila cdc14 mutants are viable, but exhibit defects in sperm competition, chemosensation, and mechanosensation.
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Affiliation(s)
- Leif R Neitzel
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Matthew R Broadus
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nailing Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Leah Sawyer
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Heather A Wallace
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Julie A Merkle
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jeanne N Jodoin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Poojitha Sitaram
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Emily E Crispi
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William Rork
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Laura A Lee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Duojia Pan
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea Page-McCaw
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA .,Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA .,Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Broadus MR, Chen TW, Neitzel LR, Ng VH, Jodoin JN, Lee LA, Salic A, Robbins DJ, Capobianco AJ, Patton JG, Huppert SS, Lee E. Identification of a Paralog-Specific Notch1 Intracellular Domain Degron. Cell Rep 2016; 15:1920-9. [PMID: 27210761 DOI: 10.1016/j.celrep.2016.04.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/14/2016] [Accepted: 04/19/2016] [Indexed: 01/13/2023] Open
Abstract
Upon Notch pathway activation, the receptor is cleaved to release the Notch intracellular domain (NICD), which translocates to the nucleus to activate gene transcription. Using Xenopus egg extracts, we have identified a Notch1-specific destruction signal (N1-Box). We show that mutations in the N1-Box inhibit NICD1 degradation and that the N1-Box is transferable for the promotion of degradation of heterologous proteins in Xenopus egg extracts and in cultured human cells. Mutation of the N1-Box enhances Notch1 activity in cultured human cells and zebrafish embryos. Human cancer mutations within the N1-Box enhance Notch1 signaling in transgenic zebrafish, highlighting the physiological relevance of this destruction signal. We find that binding of the Notch nuclear factor, CSL, to the N1-Box blocks NICD1 turnover. Our studies reveal a mechanism by which degradation of NICD1 is regulated by the N1-Box to minimize stochastic flux and to establish a threshold for Notch1 pathway activation.
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Affiliation(s)
- Matthew R Broadus
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tony W Chen
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Leif R Neitzel
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Victoria H Ng
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeanne N Jodoin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Laura A Lee
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David J Robbins
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anthony J Capobianco
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Stacey S Huppert
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt Medical Center, Nashville, TN 37232, USA.
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Abstract
Screens for small-molecule modulators of biological pathways typically utilize cultured cell lines, purified proteins, or, recently, model organisms (e.g., zebrafish, Drosophila, C. elegans). Herein, we describe a method for using Xenopus laevis egg extract, a biologically active and highly tractable cell-free system that recapitulates a legion of complex chemical reactions found in intact cells. Specifically, we focus on the use of a luciferase-based fusion system to identify small-molecule modulators that affect protein turnover.
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Affiliation(s)
- Matthew R Broadus
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, 465 21st Avenue South, U-4213A Learned Lab/MRBIII, Nashville, TN, 37232-8240, USA
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Abstract
Xenopus laevis egg extract is a well-characterized, robust system for studying the biochemistry of diverse cellular processes. Xenopus egg extract has been used to study protein turnover in many cellular contexts, including the cell cycle and signal transduction pathways(1-3). Herein, a method is described for isolating Xenopus egg extract that has been optimized to promote the degradation of the critical Wnt pathway component, β-catenin. Two different methods are described to assess β-catenin protein degradation in Xenopus egg extract. One method is visually informative ([(35)S]-radiolabeled proteins), while the other is more readily scaled for high-throughput assays (firefly luciferase-tagged fusion proteins). The techniques described can be used to, but are not limited to, assess β-catenin protein turnover and identify molecular components contributing to its turnover. Additionally, the ability to purify large volumes of homogenous Xenopus egg extract combined with the quantitative and facile readout of luciferase-tagged proteins allows this system to be easily adapted for high-throughput screening for modulators of β-catenin degradation.
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Affiliation(s)
- Tony W Chen
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University Medical Center
| | - Matthew R Broadus
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University Medical Center
| | - Stacey S Huppert
- Division of Gastroenterology, Hepatology & Nutrition and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center
| | - Ethan Lee
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University Medical Center; Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine;
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Chen JS, Broadus MR, McLean JR, Feoktistova A, Ren L, Gould KL. Comprehensive proteomics analysis reveals new substrates and regulators of the fission yeast clp1/cdc14 phosphatase. Mol Cell Proteomics 2013; 12:1074-86. [PMID: 23297348 DOI: 10.1074/mcp.m112.025924] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The conserved family of Cdc14 phosphatases targets cyclin-dependent kinase substrates in yeast, mediating late mitotic signaling events. To discover substrates and regulators of the Schizosaccharomyces pombe Cdc14 phosphatase Clp1, TAP-tagged Clp1, and a substrate trapping mutant (Clp1-C286S) were purified from asynchronous and mitotic (prometaphase and anaphase) cells and binding partners were identified by 2D-LC-MS/MS. Over 100 Clp1-interacting proteins were consistently identified, over 70 of these were enriched in Clp1-C286S-TAP (potential substrates) and we and others detected Cdk1 phosphorylation sites in over half (44/73) of these potential substrates. According to GO annotations, Clp1-interacting proteins are involved in many essential cellular processes including mitosis, cytokinesis, ribosome biogenesis, transcription, and trafficking among others. We confirmed association and dephosphorylation of multiple candidate substrates, including a key scaffolding component of the septation initiation network called Cdc11, an essential kinase of the conserved morphogenesis-related NDR kinase network named Shk1, and multiple Mlu1-binding factor transcriptional regulators. In addition, we identified Sal3, a nuclear β-importin, as the sole karyopherin required for Clp1 nucleoplasmic shuttling, a key mode of Cdc14 phosphatase regulation. Finally, a handful of proteins were more abundant in wild type Clp1-TAP versus Clp1-C286S-TAP, suggesting that they may directly regulate Clp1 signaling or serve as scaffolding platforms to localize Clp1 activity.
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Affiliation(s)
- Jun-Song Chen
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 1161 21 Avenue South, MCN B2309, Nashville, Tennessee 37232, USA
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Abstract
Nucleolar release of Cdc14 phosphatases allows them access to substrates. Multiple kinases directly affect the Clp1/Cdc14 phosphostate and the nucleolar to nucleoplasmic transition of Clp1 in fission yeast upon genotoxic stress. In addition, Clp1 regulates its own nucleolar sequestration by antagonizing a subset of these networks. The Cdc14 phosphatase family antagonizes Cdk1 phosphorylation and is important for mitotic exit. To access their substrates, Cdc14 phosphatases are released from nucleolar sequestration during mitosis. Clp1/Flp1, the Schizosaccharomyces pombe Cdc14 orthologue, and Cdc14B, a mammalian orthologue, also exit the nucleolus during interphase upon DNA replication stress or damage, respectively, implicating Cdc14 phosphatases in the response to genotoxic insults. However, a mechanistic understanding of Cdc14 phosphatase nucleolar release under these conditions is incomplete. We show here that relocalization of Clp1 during genotoxic stress is governed by complex phosphoregulation. Specifically, the Rad3 checkpoint effector kinases Cds1 and/or Chk1, the cell wall integrity mitogen-activated protein kinase Pmk1, and the cell cycle kinase Cdk1 directly phosphorylate Clp1 to promote genotoxic stress–induced nucleoplasmic accumulation. However, Cds1 and/or Chk1 phosphorylate RxxS sites preferentially upon hydroxyurea treatment, whereas Pmk1 and Cdk1 preferentially phosphorylate Clp1 TP sites upon H2O2 treatment. Abolishing both Clp1 RxxS and TP phosphosites eliminates any genotoxic stress–induced redistribution. Reciprocally, preventing dephosphorylation of Clp1 TP sites shifts the distribution of the enzyme to the nucleoplasm constitutively. This work advances our understanding of pathways influencing Clp1 localization and may provide insight into mechanisms controlling Cdc14B phosphatases in higher eukaryotes.
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Affiliation(s)
- Matthew R Broadus
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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