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Behera A, Reddy ABM. WWP1 E3 ligase at the crossroads of health and disease. Cell Death Dis 2023; 14:853. [PMID: 38129384 PMCID: PMC10739765 DOI: 10.1038/s41419-023-06380-0] [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: 04/21/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The E3 ubiquitin ligase WWP1 (WW Domain-containing E3 Ubiquitin Protein Ligase 1) is a member of the HECT (Homologous to the E6-associated protein Carboxyl Terminus) E3 ligase family. It is conserved across several species and plays crucial roles in various physiological processes, including development, cell growth and proliferation, apoptosis, and differentiation. It exerts its functions through ubiquitination or protein-protein interaction with PPXY-containing proteins. WWP1 plays a role in several human diseases, including cardiac conditions, neurodevelopmental, age-associated osteogenic disorders, infectious diseases, and cancers. In solid tumors, WWP1 plays a dual role as both an oncogene and a tumor suppressor, whereas in hematological malignancies such as AML, it is identified as a dedicated oncogene. Importantly, WWP1 inhibition using small molecule inhibitors such as Indole-3-Carbinol (I3C) and Bortezomib or siRNAs leads to significant suppression of cancer growth and healing of bone fractures, suggesting that WWP1 might serve as a potential therapeutic target for several diseases. In this review, we discuss the evolutionary perspective, structure, and functions of WWP1 and its multilevel regulation by various regulators. We also examine its emerging roles in cancer progression and its therapeutic potential. Finally, we highlight WWP1's role in normal physiology, contribution to pathological conditions, and therapeutic potential for cancer and other diseases.
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Affiliation(s)
- Abhayananda Behera
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
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2
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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [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: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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3
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Sullivan KG, Bashaw GJ. Commissureless acts as a substrate adapter in a conserved Nedd4 E3 ubiquitin ligase pathway to promote axon growth across the midline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562283. [PMID: 37905056 PMCID: PMC10614773 DOI: 10.1101/2023.10.13.562283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In both vertebrates and invertebrates, commissural neurons prevent premature responsiveness to the midline repellant Slit by downregulating surface levels of its receptor Roundabout1 (Robo1). In Drosophila, Commissureless (Comm) plays a critical role in this process; however, there is conflicting data on the underlying molecular mechanism. Here, we demonstrate that the conserved PY motifs in the cytoplasmic domain of Comm are required allow the ubiquitination and lysosomal degradation of Robo1. Disruption of these motifs prevents Comm from localizing to Lamp1 positive late endosomes and to promote axon growth across the midline in vivo. In addition, we conclusively demonstrate a role for Nedd4 in midline crossing. Genetic analysis shows that nedd4 mutations result in midline crossing defects in the Drosophila embryonic nerve cord, which can be rescued by introduction of exogenous Nedd4. Biochemical evidence shows that Nedd4 incorporates into a three-member complex with Comm and Robo in a PY motif-dependent manner. Finally, we present genetic evidence that Nedd4 acts with Comm in the embryonic nerve cord to downregulate Robo1 levels. Taken together, these findings demonstrate that Comm promotes midline crossing in the nerve cord by facilitating Robo ubiquitination by Nedd4, ultimately leading to its degradation.
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Affiliation(s)
- Kelly G. Sullivan
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd., Philadelphia, PA, 19104, USA
| | - Greg J. Bashaw
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd., Philadelphia, PA, 19104, USA
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4
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Bardwell AJ, Paul M, Yoneda KC, Andrade-Ludeña MD, Nguyen OT, Fruman DA, Bardwell L. The WW domain of IQGAP1 binds directly to the p110α catalytic subunit of PI 3-kinase. Biochem J 2023; 480:BCJ20220493. [PMID: 37145016 PMCID: PMC10625650 DOI: 10.1042/bcj20220493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/06/2023]
Abstract
IQGAP1 is a multi-domain cancer-associated protein that serves as a scaffold protein for multiple signaling pathways. Numerous binding partners have been found for the calponin homology, IQ and GAP-related domains in IQGAP1. Identification of a binding partner for its WW domain has proven elusive, however, even though a cell-penetrating peptide derived from this domain has marked anti-tumor activity. Here, using in vitro binding assays with human proteins and co-precipitation from human cells, we show that the WW domain of human IQGAP1 binds directly to the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K). In contrast, the WW domain does not bind to ERK1/2, MEK1/2, or the p85α regulatory subunit of PI3K when p85α is expressed alone. However, the WW domain is able to bind to the p110α/p85α heterodimer when both subunits are co-expressed, as well as to the mutationally activated p110α/p65α heterodimer. We present a model of the structure of the IQGAP1 WW domain, and experimentally identify key residues in the hydrophobic core and beta strands of the WW domain that are required for binding to p110α. These findings contribute to a more precise understanding of IQGAP1-mediated scaffolding, and of how IQGAP1-derived therapeutic peptides might inhibit tumorigenesis.
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Affiliation(s)
- A. Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | - Madhuri Paul
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, U.S.A
| | - Kiku C. Yoneda
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | | | - Oanh T. Nguyen
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | - David A. Fruman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, U.S.A
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
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5
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Castillo F, Corbi-Verge C, Murciano-Calles J, Candel AM, Han Z, Iglesias-Bexiga M, Ruiz-Sanz J, Kim PM, Harty RN, Martinez JC, Luque I. Phage display identification of nanomolar ligands for human NEDD4-WW3: Energetic and dynamic implications for the development of broad-spectrum antivirals. Int J Biol Macromol 2022; 207:308-323. [PMID: 35257734 DOI: 10.1016/j.ijbiomac.2022.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
The recognition of PPxY viral Late domains by the third WW domain of the human HECT-E3 ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses. Blocking these interactions is a promising strategy to develop broad-spectrum antivirals. As all WW domains, NEDD4-WW3 is a challenging therapeutic target due to the low binding affinity of its natural interactions, its high conformational plasticity, and its complex thermodynamic behavior. In this work, we set out to investigate whether high affinity can be achieved for monovalent ligands binding to the isolated NEDD4-WW3 domain. We show that a competitive phage-display set-up allows for the identification of high-affinity peptides showing inhibitory activity of viral budding. A detailed biophysical study combining calorimetry, nuclear magnetic resonance, and molecular dynamic simulations reveals that the improvement in binding affinity does not arise from the establishment of new interactions with the domain, but is associated to conformational restrictions imposed by a novel C-terminal -LFP motif in the ligand, unprecedented in the PPxY interactome. These results, which highlight the complexity of WW domain interactions, provide valuable insight into the key elements for high binding affinity, of interest to guide virtual screening campaigns for the identification of novel therapeutics targeting NEDD4-WW3 interactions.
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Affiliation(s)
- Francisco Castillo
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Carles Corbi-Verge
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain; Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics & Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Javier Murciano-Calles
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Adela M Candel
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Ziying Han
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Manuel Iglesias-Bexiga
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics & Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ronald N Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Jose C Martinez
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Irene Luque
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
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6
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Martinez JC, Castillo F, Ruiz-Sanz J, Murciano-Calles J, Camara-Artigas A, Luque I. Understanding binding affinity and specificity of modular protein domains: A focus in ligand design for the polyproline-binding families. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:161-188. [PMID: 35534107 DOI: 10.1016/bs.apcsb.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Within the modular protein domains there are five families that recognize proline-rich sequences: SH3, WW, EVH1, GYF and UEV domains. This chapter reviews the main strategies developed for the design of ligands for these families, including peptides, peptidomimetics and drugs. We also describe some studies aimed to understand the molecular reasons responsible for the intrinsic affinity and specificity of these domains.
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Affiliation(s)
- Jose C Martinez
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Castillo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Javier Ruiz-Sanz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Javier Murciano-Calles
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Ana Camara-Artigas
- Departamento de Química Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario ceiA3 y CIAMBITAL, Almeria, Spain
| | - Irene Luque
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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7
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Chen F, Wang Q, Mu Y, Sun S, Yuan X, Shang P, Ji B. Systematic profiling and identification of the peptide-mediated interactions between human Yes-associated protein and its partners in esophageal cancer. J Mol Recognit 2021; 35:e2947. [PMID: 34964176 DOI: 10.1002/jmr.2947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
Human Yes-associated protein (YAP) is involved in the Hippo signaling pathway and serves as a coactivator to modulate gene expression, which contains a transactivation domain (TD) responsible for binding to the downstream TEA domain family (TEAD) of transcription factors and two WW1/2 domains that recognize the proline-rich motifs (PRMs) present in a variety of upstream protein partners through peptide-mediated interactions (PMIs). The downstream YAP TD-TEAD interactions are closely associated with gastric cancer, and a number of therapeutic agents have been developed to target the interactions. In contrast, the upstream YAP WW1/2-partner interactions are thought to be involved in esophageal cancer but still remain largely unexplored. Here, we attempted to elucidate the complicated PMIs between the YAP WW1/2 domains and various PRMs of YAP-interacting proteins. A total of 106 peptide segments carrying the class I WW-binding motif [P/L]Px[Y/P] were extracted from 22 partner candidates, which are potential recognition sites of YAP WW1/2 domains. Structural and energetic analyses of the intermolecular interactions between the domains and peptides created a systematic domain-peptide binding profile, from which a number of biologically functional PMIs were identified and then substantiated in vitro using fluorescence spectroscopy assays. It is revealed that: (a) The sequence requirement for the partner recognition site binding to YAP WW1/2 domains is a decapeptide segment that contains a core PRM motif as well as two three-residue extensions from each side of the motif; the core motif and extended sections are responsible for the binding stability and recognition specificity of domain-peptide interaction, respectively. (b) There is an exquisite difference in the recognition specificity of the two domains; the LPxP and PPxP appear to more prefer WW1 than WW2, whereas the WW2 can bind more effectively to LPxY and PPxY than WW1. (c) WW2 generally exhibits a higher affinity to the panel of recognition site candidates than WW1. In addition, a number of partner peptides were found as promising recognition sites of the two domains and/or to have a good selectivity between the two domains. For example, the DVL1 peptide was determined to have moderate affinity to WW2 and strong selectivity for WW2 over WW1. Hydrogen bonds play a central role in selectivity.
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Affiliation(s)
- Fei Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Qifei Wang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Yushu Mu
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Shibin Sun
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Xulong Yuan
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Pan Shang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Bo Ji
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
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8
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Wang Y, Du Y, Luo L, Hu P, Yang G, Li T, Han X, Ma A, Wang T. Alterations of Nedd4-2-binding capacity in PY-motif of Na V 1.5 channel underlie long QT syndrome and Brugada syndrome. Acta Physiol (Oxf) 2020; 229:e13438. [PMID: 31900993 DOI: 10.1111/apha.13438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/19/2019] [Accepted: 12/29/2019] [Indexed: 12/13/2022]
Abstract
AIMS Pathogenic variants of the SCN5A gene can cause Brugada syndrome (BrS) and long QT syndrome (LQTS), which predispose individuals to potentially fatal ventricular arrhythmias and sudden cardiac death. SCN5A encodes the NaV 1.5 protein, the pore forming α-subunit of the voltage-dependent cardiac Na+ channel. Using a WW domain, the E3 ubiquitin ligase Nedd4-2 binds to the PY-motif ([L/P]PxY) within the C-terminus of NaV 1.5, which results in decreased protein expression and current through NaV 1.5 ubiquitination. Here, we investigate the role of E3 ubiquitin ligase Nedd4-2-mediated NaV 1.5 degradation in the pathological mechanisms of the BrS-associated variant SCN5A-p.L1239P and LQTS-associated variant SCN5A-p.Y1977N. METHODS AND RESULTS Using a combination of molecular biology, biochemical and electrophysiological approaches, we examined the expression, function and Nedd4-2 interactions of SCN5A-p.L1239P and SCN5A-p.Y1977N. SCN5A-p.L1239P is characterized as a loss-of-function, whereas SCN5A-p.Y1977N is a gain-of-function variant of the NaV 1.5 channel. Sequence alignment shows that BrS-associated SCN5A-p.L1239P has a new Nedd4-2-binding site (from LLxY to LPxY). This new Nedd4-2-binding site increases the interaction between NaV 1.5 and Nedd4-2, enhancing ubiquitination and degradation of the NaV 1.5 channel. Disruption of the new Nedd4-2-binding site of SCN5A-p.L1239P restores NaV 1.5 expression and function. However, the LQTS-associated SCN5A-p.Y1977N disrupts the usual Nedd4-2-binding site (from PPxY to PPxN). This decreases NaV 1.5-Nedd4-2 interaction, preventing ubiquitination and degradation of NaV 1.5 channels. CONCLUSIONS Our data suggest that the PY-motif plays an essential role in modifying the expression/function of NaV 1.5 channels through Nedd4-2-mediated ubiquitination. Alterations of NaV 1.5-Nedd4-2 interaction represent a novel pathological mechanism for NaV 1.5 channel diseases caused by SCN5A variants.
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Affiliation(s)
- Ya Wang
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Yuan Du
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Ling Luo
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Peijing Hu
- Department of Cardiovascular Medicine Second Affiliated Hospital of Xi'an Medical College Xi'an Shaanxi P. R. China
| | - Guodong Yang
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Tao Li
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Xiu Han
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
| | - Aiqun Ma
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
- Key Laboratory of Molecular Cardiology Xi'an Shaanxi P. R. China
- Key Laboratory of Environment and Genes Related to Diseases Xi'an Jiaotong University Ministry of Education Xi'an Shaanxi P. R. China
| | - Tingzhong Wang
- Department of Cardiovascular Medicine First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi P. R. China
- Key Laboratory of Molecular Cardiology Xi'an Shaanxi P. R. China
- Key Laboratory of Environment and Genes Related to Diseases Xi'an Jiaotong University Ministry of Education Xi'an Shaanxi P. R. China
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9
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Binding site plasticity in viral PPxY Late domain recognition by the third WW domain of human NEDD4. Sci Rep 2019; 9:15076. [PMID: 31636332 PMCID: PMC6803667 DOI: 10.1038/s41598-019-50701-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022] Open
Abstract
The recognition of PPxY viral Late domains by the third WW domain of the HECT-E3 ubiquitin ligase NEDD4 (hNEDD4-WW3) is essential for the completion of the budding process of numerous enveloped viruses, including Ebola, Marburg, HTLV1 or Rabies. hNEDD4-WW3 has been validated as a promising target for the development of novel host-oriented broad spectrum antivirals. Nonetheless, finding inhibitors with good properties as therapeutic agents remains a challenge since the key determinants of binding affinity and specificity are still poorly understood. We present here a detailed structural and thermodynamic study of the interactions of hNEDD4-WW3 with viral Late domains combining isothermal titration calorimetry, NMR structural determination and molecular dynamics simulations. Structural and energetic differences in Late domain recognition reveal a highly plastic hNEDD4-WW3 binding site that can accommodate PPxY-containing ligands with varying orientations. These orientations are mostly determined by specific conformations adopted by residues I859 and T866. Our results suggest a conformational selection mechanism, extensive to other WW domains, and highlight the functional relevance of hNEDD4-WW3 domain conformational flexibility at the binding interface, which emerges as a key element to consider in the search for potent and selective inhibitors of therapeutic interest.
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10
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Wawrzycka D, Sadlak J, Maciaszczyk-Dziubinska E, Wysocki R. Rsp5-dependent endocytosis and degradation of the arsenite transporter Acr3 requires its N-terminal acidic tail as an endocytic sorting signal and arrestin-related ubiquitin-ligase adaptors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:916-925. [PMID: 30776335 DOI: 10.1016/j.bbamem.2019.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 01/15/2023]
Abstract
The yeast plasma membrane transporter Acr3 mediates efflux of toxic arsenite and antimonite. Here, we investigated the mechanisms of Acr3 turnover. We found that after arrival and residence at the plasma membrane, Acr3 is subjected to internalization followed by proteolysis in the vacuole. Endocytic degradation of Acr3 is promoted by the ubiquitin ligase Rsp5 and requires polyubiquitination of Acr3 at multiple lysine residues via lysine 63-linked ubiquitin chains. The turnover of Acr3 also depends on two arrestin-related proteins, Art3/Aly2 and Art4/Rod1, that enable recruitment of Rsp5 to its targets. Finally, we found that a short acidic patch located in the N-terminal tail of Acr3 is needed for its ubiquitination and internalization. We propose that this motif serves as an endocytic signal that facilitates binding of the arrestin-Rsp5 complexes to the Acr3 cargo.
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Affiliation(s)
- Donata Wawrzycka
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Joanna Sadlak
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | | | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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11
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Abstract
Nedd4 is a family of ubiquitin E3 ligases that regulate numerous cellular processes. In this report, we showed that alpha- and beta-herpesviruses have membrane proteins that regulate the function of the Nedd4 family members. Although the homology search score was quite low, UL56 of herpes simplex virus type 1 and 2, ORF0 of varicella-zoster virus, UL42 of human cytomegalovirus, and U24 of human herpesvirus 6A, 6B, and 7 all possess at least one PPxY (PY) motif in their cytoplasmic domain, and are able to bind with Itch, a member of the Nedd4 family. These viral proteins altered the localization of Itch and decreased Itch expression in co-expressing cells. In addition, these viral proteins reduced the production of retrovirus vectors through the regulation of the Nedd4 family of proteins. U24, but not the other proteins, effectively reduced CD3ε expression on the T cell surface. These viral molecules are thought to contribute to the specific function of each virus through the regulation of Nedd4 family activity.
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12
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Justice ED, Barnum SJ, Kidd T. The WAGR syndrome gene PRRG4 is a functional homologue of the commissureless axon guidance gene. PLoS Genet 2017; 13:e1006865. [PMID: 28859078 PMCID: PMC5578492 DOI: 10.1371/journal.pgen.1006865] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/11/2017] [Indexed: 01/20/2023] Open
Abstract
WAGR syndrome is characterized by Wilm's tumor, aniridia, genitourinary abnormalities and intellectual disabilities. WAGR is caused by a chromosomal deletion that includes the PAX6, WT1 and PRRG4 genes. PRRG4 is proposed to contribute to the autistic symptoms of WAGR syndrome, but the molecular function of PRRG4 genes remains unknown. The Drosophila commissureless (comm) gene encodes a short transmembrane protein characterized by PY motifs, features that are shared by the PRRG4 protein. Comm intercepts the Robo axon guidance receptor in the ER/Golgi and targets Robo for degradation, allowing commissural axons to cross the CNS midline. Expression of human Robo1 in the fly CNS increases midline crossing and this was enhanced by co-expression of PRRG4, but not CYYR, Shisa or the yeast Rcr genes. In cell culture experiments, PRRG4 could re-localize hRobo1 from the cell surface, suggesting that PRRG4 is a functional homologue of Comm. Comm is required for axon guidance and synapse formation in the fly, so PRRG4 could contribute to the autistic symptoms of WAGR by disturbing either of these processes in the developing human brain.
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Affiliation(s)
- Elizabeth D. Justice
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
| | - Sarah J. Barnum
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
| | - Thomas Kidd
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
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13
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Panwalkar V, Neudecker P, Willbold D, Dingley AJ. Multiple WW domains of Nedd4-1 undergo conformational exchange that is quenched upon peptide binding. FEBS Lett 2017; 591:1573-1583. [DOI: 10.1002/1873-3468.12664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Vineet Panwalkar
- ICS-6 (Strukturbiochemie); Forschungszentrum Jülich; Germany
- Institut für Physikalische Biologie; Heinrich-Heine-Universität; Düsseldorf Germany
| | - Philipp Neudecker
- ICS-6 (Strukturbiochemie); Forschungszentrum Jülich; Germany
- Institut für Physikalische Biologie; Heinrich-Heine-Universität; Düsseldorf Germany
| | - Dieter Willbold
- ICS-6 (Strukturbiochemie); Forschungszentrum Jülich; Germany
- Institut für Physikalische Biologie; Heinrich-Heine-Universität; Düsseldorf Germany
| | - Andrew J. Dingley
- ICS-6 (Strukturbiochemie); Forschungszentrum Jülich; Germany
- Institut für Physikalische Biologie; Heinrich-Heine-Universität; Düsseldorf Germany
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14
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Vélez P, Schwartz AB, Iyer SR, Warrington A, Fadool DA. Ubiquitin ligase Nedd4-2 modulates Kv1.3 current amplitude and ion channel protein targeting. J Neurophysiol 2016; 116:671-85. [PMID: 27146988 DOI: 10.1152/jn.00874.2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 05/04/2016] [Indexed: 11/22/2022] Open
Abstract
Voltage-dependent potassium channels (Kv) go beyond the stabilization of the resting potential and regulate biochemical pathways, regulate intracellular signaling, and detect energy homeostasis. Because targeted deletion and pharmacological block of the Kv1.3 channel protein produce marked changes in metabolism, resistance to diet-induced obesity, and changes in olfactory structure and function, this investigation explored Nedd4-2-mediated ubiquitination and degradation to regulate Kv1.3 channel density. Heterologous coexpression of Nedd4-2 ligase and Kv1.3 in HEK 293 cells reduced Kv1.3 current density without modulation of kinetic properties as measured by patch-clamp electrophysiology. Modulation of current density was dependent on ligase activity and was lost through point mutation of cysteine 938 in the catalytic site of the ligase (Nedd4-2CS). Incorporation of adaptor protein Grb10 relieved Nedd4-2-induced current suppression as did application of the proteasome inhibitor Mg-132. SDS-PAGE and immunoprecipitation strategies demonstrated a channel/adaptor/ligase signalplex. Pixel immunodensity was reduced for Kv1.3 in the presence of Nedd4-2, which was eliminated upon additional incorporation of Grb10. We confirmed Nedd4-2/Grb10 coimmunoprecipitation and observed an increased immunodensity for Nedd4-2 in the presence of Kv1.3 plus Grb10, regardless of whether the catalytic site was active. Kv1.3/Nedd4-2 were reciprocally coimmunoprecipated, whereby mutation of the COOH-terminal, SH3-recognition (493-498), or ubiquitination sites on Kv1.3 (lysines 467, 476, 498) retained coimmunoprecipitation, while the latter prevented the reduction in channel density. A model is presented for which an atypical interaction outside the canonical PY motif may permit channel/ligase interaction to lead to protein degradation and reduced current density, which can involve Nedd4-2/Grb10 interactions to disrupt Kv1.3 loss of current density.
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Affiliation(s)
- Patricio Vélez
- Program in Neuroscience, Florida State University, Tallahassee, Florida
| | - Austin B Schwartz
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; and
| | - Subashini R Iyer
- Program in Neuroscience, Florida State University, Tallahassee, Florida
| | - Anthony Warrington
- Department of Biological Sciences, Florida State University, Tallahassee, Florida
| | - Debra Ann Fadool
- Program in Neuroscience, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; and Department of Biological Sciences, Florida State University, Tallahassee, Florida
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15
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Shah J, Guerrera D, Vasileva E, Sluysmans S, Bertels E, Citi S. PLEKHA7: Cytoskeletal adaptor protein at center stage in junctional organization and signaling. Int J Biochem Cell Biol 2016; 75:112-6. [PMID: 27072621 DOI: 10.1016/j.biocel.2016.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
Abstract
PLEKHA7 is a recently characterized component of the cytoplasmic region of epithelial adherens junctions (AJ). It comprises two WW domains, a pleckstrin-homology domain, and proline-rich and coiled-coil domains. PLEKHA7 interacts with cytoplasmic components of the AJ (p120-catenin, paracingulin, afadin), stabilizes the E-cadherin complex by linking it to the minus ends of noncentrosomal microtubules, and stabilizes junctional nectins through the newly identified interactor PDZD11. Similarly to afadin, and unlike E-cadherin and p120-catenin, the localization of PLEKHA7 at AJ is strictly zonular (in the zonula adhaerens subdomain of AJ), and does not extend along the basolateral contacts. Genome-wide association studies and experiments on animal and cellular models show that although PLEKHA7 is not required for organism viability, it is implicated in cardiovascular physiology, hypertension, primary angle closure glaucoma, susceptibility to staphylococcal α-toxin, and epithelial morphogenesis and growth. Thus, PLEKHA7 is a cytoskeletal adaptor protein important for AJ organization, and at the center of junction-associated signaling pathways which fine-tune important pathophysiological processes.
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Affiliation(s)
- Jimit Shah
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Diego Guerrera
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ekaterina Vasileva
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Sophie Sluysmans
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Eva Bertels
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Sandra Citi
- Department of Cell Biology, University of Geneva, Geneva, Switzerland; The Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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16
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Koshizuka T, Tanaka K, Suzutani T. Degradation of host ubiquitin E3 ligase Itch by human cytomegalovirus UL42. J Gen Virol 2016; 97:196-208. [DOI: 10.1099/jgv.0.000336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Tetsuo Koshizuka
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Keiichiro Tanaka
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Tatsuo Suzutani
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan
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17
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Martinez-Rodriguez S, Bacarizo J, Luque I, Camara-Artigas A. Crystal structure of the first WW domain of human YAP2 isoform. J Struct Biol 2015; 191:381-7. [DOI: 10.1016/j.jsb.2015.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 11/16/2022]
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Abstract
Endocytosis, the process whereby the plasma membrane invaginates to form vesicles, is essential for bringing many substances into the cell and for membrane turnover. The mechanism driving clathrin-mediated endocytosis (CME) involves > 50 different protein components assembling at a single location on the plasma membrane in a temporally ordered and hierarchal pathway. These proteins perform precisely choreographed steps that promote receptor recognition and clustering, membrane remodeling, and force-generating actin-filament assembly and turnover to drive membrane invagination and vesicle scission. Many critical aspects of the CME mechanism are conserved from yeast to mammals and were first elucidated in yeast, demonstrating that it is a powerful system for studying endocytosis. In this review, we describe our current mechanistic understanding of each step in the process of yeast CME, and the essential roles played by actin polymerization at these sites, while providing a historical perspective of how the landscape has changed since the preceding version of the YeastBook was published 17 years ago (1997). Finally, we discuss the key unresolved issues and where future studies might be headed.
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Affiliation(s)
- Bruce L Goode
- Brandeis University, Department of Biology, Rosenstiel Center, Waltham, Massachusetts 02454
| | - Julian A Eskin
- Brandeis University, Department of Biology, Rosenstiel Center, Waltham, Massachusetts 02454
| | - Beverly Wendland
- The Johns Hopkins University, Department of Biology, Baltimore, Maryland 21218
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19
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Iglesias-Bexiga M, Castillo F, Cobos ES, Oka T, Sudol M, Luque I. WW domains of the yes-kinase-associated-protein (YAP) transcriptional regulator behave as independent units with different binding preferences for PPxY motif-containing ligands. PLoS One 2015; 10:e0113828. [PMID: 25607641 PMCID: PMC4301871 DOI: 10.1371/journal.pone.0113828] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 10/31/2014] [Indexed: 12/28/2022] Open
Abstract
YAP is a WW domain-containing effector of the Hippo tumor suppressor pathway, and the object of heightened interest as a potent oncogene and stemness factor. YAP has two major isoforms that differ in the number of WW domains they harbor. Elucidating the degree of co-operation between these WW domains is important for a full understanding of the molecular function of YAP. We present here a detailed biophysical study of the structural stability and binding properties of the two YAP WW domains aimed at investigating the relationship between both domains in terms of structural stability and partner recognition. We have carried out a calorimetric study of the structural stability of the two YAP WW domains, both isolated and in a tandem configuration, and their interaction with a set of functionally relevant ligands derived from PTCH1 and LATS kinases. We find that the two YAP WW domains behave as independent units with different binding preferences, suggesting that the presence of the second WW domain might contribute to modulate target recognition between the two YAP isoforms. Analysis of structural models and phage-display studies indicate that electrostatic interactions play a critical role in binding specificity. Together, these results are relevant to understand of YAP function and open the door to the design of highly specific ligands of interest to delineate the functional role of each WW domain in YAP signaling.
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Affiliation(s)
- Manuel Iglesias-Bexiga
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Francisco Castillo
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Eva S. Cobos
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Tsutomu Oka
- Weis Center for Research, Geisinger Clinic, M.C. 26–08, 100 North Academy Avenue, Danville, PA, 17822–2608, United States of America
| | - Marius Sudol
- Weis Center for Research, Geisinger Clinic, M.C. 26–08, 100 North Academy Avenue, Danville, PA, 17822–2608, United States of America
| | - Irene Luque
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- * E-mail:
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20
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Mujoo K, Choi BK, Huang Z, Zhang N, An Z. Regulation of ERBB3/HER3 signaling in cancer. Oncotarget 2014; 5:10222-36. [PMID: 25400118 PMCID: PMC4279368 DOI: 10.18632/oncotarget.2655] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/02/2014] [Indexed: 12/18/2022] Open
Abstract
ERBB3/HER3 is emerging as a molecular target for various cancers. HER3 is overexpressed and activated in a number of cancer types under the conditions of acquired resistance to other HER family therapeutic interventions such as tyrosine kinase inhibitors and antibody therapies. Regulation of the HER3 expression and signaling involves numerous HER3 interacting proteins. These proteins include PI3K, Shc, and E3 ubiquitin ligases NEDD4 and Nrdp1. Furthermore, recent identification of a number of HER3 oncogenic mutations in colon and gastric cancers elucidate the role of HER3 in cancer development. Despite the strong evidence regarding the role of HER3 in cancer, the current understanding of the regulation of HER3 expression and activation requires additional research. Moreover, the lack of biomarkers for HER3-driven cancer poses a big challenge for the clinical development of HER3 targeting antibodies. Therefore, a better understanding of HER3 regulation should improve the strategies to therapeutically target HER3 for cancer therapy.
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Affiliation(s)
- Kalpana Mujoo
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
- Current address: Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX
| | - Byung-Kwon Choi
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Zhao Huang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
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21
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Abstract
Ion channel proteins are regulated by different types of posttranslational modifications. The focus of this review is the regulation of voltage-gated sodium channels (Navs) upon their ubiquitylation. The amiloride-sensitive epithelial sodium channel (ENaC) was the first ion channel shown to be regulated upon ubiquitylation. This modification results from the binding of ubiquitin ligase from the Nedd4 family to a protein-protein interaction domain, known as the PY motif, in the ENaC subunits. Many of the Navs have similar PY motifs, which have been demonstrated to be targets of Nedd4-dependent ubiquitylation, tagging them for internalization from the cell surface. The role of Nedd4-dependent regulation of the Nav membrane density in physiology and disease remains poorly understood. Two recent studies have provided evidence that Nedd4-2 is downregulated in dorsal root ganglion (DRG) neurons in both rat and mouse models of nerve injury-induced neuropathic pain. Using two different mouse models, one with a specific knockout of Nedd4-2 in sensory neurons and another where Nedd4-2 was overexpressed with the use of viral vectors, it was demonstrated that the neuropathy-linked neuronal hyperexcitability was the result of Nav1.7 and Nav1.8 overexpression due to Nedd4-2 downregulation. These studies provided the first in vivo evidence of the role of Nedd4-2-dependent regulation of Nav channels in a disease state. This ubiquitylation pathway may be involved in the development of symptoms and diseases linked to Nav-dependent hyperexcitability, such as pain, cardiac arrhythmias, epilepsy, migraine, and myotonias.
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Affiliation(s)
- Cédric J Laedermann
- Department of Clinical Research, University of Bern, Murtenstrasse, 35, 3010, Bern, Switzerland,
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22
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Abstract
Our understanding of the FERM (4.1/ezrin/radixin/moesin) protein family has been rapidly expanding in the last few years, with the result that many new physiological functions have been ascribed to these biochemically unique proteins. In the present review, we will discuss a number of new FRMD (FERM domain)-containing proteins that were initially discovered from genome sequencing but are now being established through biochemical and genetic studies to be involved both in normal cellular processes, but are also associated with a variety of human diseases.
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23
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Song F, Fan C, Wang X, Goodrich DW. The Thoc1 encoded ribonucleoprotein is a substrate for the NEDD4-1 E3 ubiquitin protein ligase. PLoS One 2013; 8:e57995. [PMID: 23460917 PMCID: PMC3584038 DOI: 10.1371/journal.pone.0057995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
Ribonucleoprotein (RNP) complexes form around nascent RNA during transcription to facilitate proper transcriptional elongation, RNA processing, and nuclear export. RNPs are highly heterogeneous, and different types of RNPs tend to package functionally related transcripts. These observations have inspired the hypothesis that RNP mediated mechanisms help specify coordinated gene expression. This hypothesis is supported by the observation that mutations in RNP components can cause defects in specific developmental pathways. How RNP biogenesis itself is regulated, however, is not well understood. The evolutionarily conserved THO RNP complex functions early during transcription to package nascent transcripts and facilitate subsequent RNP biogenesis. THO deficiency compromises transcriptional elongation as well as RNP mediated events like 3′ end formation and nuclear export for some transcripts. Using molecularly manipulated cells and in vitro reconstituted biochemical reactions, we demonstrate that the essential THO protein component encoded by the Thoc1 gene is poly-ubiquitinated by the NEDD4-1 E3 ubiquitin ligase. Poly-ubiquitinated pThoc1 is degraded by the proteasome. These results indicate THO activity is regulated by the ubiquitin-proteasome pathway, and that this regulation is evolutionarily conserved between yeast and mammals. Manipulation of NEDD4-1 levels has modest effects on Thoc1 protein levels under steady state conditions, but destabilization of Thoc1 protein upon treatment with a transcriptional elongation inhibitor is dependent on NEDD4-1. This suggests NEDD4-1 functions in conjunction with other post-translational mechanisms to regulate Thoc1 protein and THO activity.
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Affiliation(s)
- Fei Song
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Chuandong Fan
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Xinjiang Wang
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - David W. Goodrich
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
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24
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Patel S, Mathonet P, Jaulent AM, Ullman CG. Selection of a high-affinity WW domain against the extracellular region of VEGF receptor isoform-2 from a combinatorial library using CIS display. Protein Eng Des Sel 2013; 26:307-15. [PMID: 23378640 DOI: 10.1093/protein/gzt003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
WW domains are small β-sheet motifs that are involved in intracellular signalling through the recognition of proline-rich or phosphorylated linear peptide sequences. Here, we describe modification of this motif to provide a framework for engineering the side chains exposed on its concave surface. This non-natural scaffold incorporates an additional tryptophan, has a shorter loop 1 and supports modification of 25% of the natural protein to form a novel affinity reagent. We demonstrate the utility of this structure by selecting a high-affinity binder to the extracellular region of human vascular endothelial growth factor receptor isoform 2 (VEGFR-2) from a library of modifications, using a cell-free molecular display platform, CIS display. The isolate has low nanomolar affinity to VEGFR-2 and inhibits binding of human VEGF to its receptor with nanomolar activity. The structure is amenable to cyclisation to improve its proteolytic stability and has advantages over larger protein scaffolds in that it can be synthesised chemically to high yields offering potential for therapeutic and non-therapeutic applications.
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Affiliation(s)
- Seema Patel
- Isogenica Ltd, Little Chesterford, Essex CB10 1XL, UK
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25
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Guo Z, Song E, Ma S, Wang X, Gao S, Shao C, Hu S, Jia L, Tian R, Xu T, Gao Y. Proteomics strategy to identify substrates of LNX, a PDZ domain-containing E3 ubiquitin ligase. J Proteome Res 2012; 11:4847-62. [PMID: 22889411 DOI: 10.1021/pr300674c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin ligases (E3s) confer specificity to ubiquitination by recognizing target substrates. However, the substrates of most E3s have not been extensively discovered, and new methods are needed to efficiently and comprehensively identify these substrates. Mostly, E3s specifically recognize substrates via their protein interaction domains. We developed a novel integrated strategy to identify substrates of E3s containing protein interaction domains on a proteomic scale. The binding properties of the protein interaction domains were characterized by screening a random peptide library using a yeast two-hybrid system. Artificial degrons, consisting of a preferential ubiquitination sequence and particular interaction domain-binding motifs, were tested as potential substrates by in vitro ubiquitination assays. Using this strategy, not only substrates but also nonsubstrate regulators can be discovered. The detailed substrate recognition mechanisms, which are useful for drug discovery, can also be characterized. We used the Ligand of Numb protein X (LNX) family of E3s, a group of PDZ domain-containing RING-type E3 ubiquitin ligases, to demonstrate the feasibility of this strategy. Many potential substrates of LNX E3s were identified. Eight of the nine selected candidates were ubiquitinated in vitro, and two novel endogenous substrates, PDZ-binding kinase (PBK) and breakpoint cluster region protein (BCR), were confirmed in vivo. We further revealed that the LNX1-mediated ubiquitination and degradation of PBK inhibited cell proliferation and enhanced sensitivity to doxorubicin-induced apoptosis. The substrate recognition mechanism of LNX E3s was also characterized; this process involves the recognition of substrates via their specific PDZ domains by binding to the C-termini of the target proteins. This strategy can potentially be extended to a variety of E3s that contain protein interaction domain(s), thereby serving as a powerful tool for the comprehensive identification of their substrates on a proteomic scale.
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Affiliation(s)
- Zhengguang Guo
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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26
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Terabayashi T, Sakaguchi M, Shinmyozu K, Ohshima T, Johjima A, Ogura T, Miki H, Nishinakamura R. Phosphorylation of Kif26b promotes its polyubiquitination and subsequent proteasomal degradation during kidney development. PLoS One 2012; 7:e39714. [PMID: 22768111 PMCID: PMC3387196 DOI: 10.1371/journal.pone.0039714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 05/25/2012] [Indexed: 01/24/2023] Open
Abstract
Kif26b, a member of the kinesin superfamily proteins (KIFs), is essential for kidney development. Kif26b expression is restricted to the metanephric mesenchyme, and its transcription is regulated by a zinc finger transcriptional regulator Sall1. However, the mechanism(s) by which Kif26b protein is regulated remain unknown. Here, we demonstrate phosphorylation and subsequent polyubiquitination of Kif26b in the developing kidney. We find that Kif26b interacts with an E3 ubiquitin ligase, neural precursor cell expressed developmentally down-regulated protein 4 (Nedd4) in developing kidney. Phosphorylation of Kif26b at Thr-1859 and Ser-1962 by the cyclin-dependent kinases (CDKs) enhances the interaction of Kif26b with Nedd4. Nedd4 polyubiquitinates Kif26b and thereby promotes degradation of Kif26b via the ubiquitin-proteasome pathway. Furthermore, Kif26b lacks ATPase activity but does associate with microtubules. Nocodazole treatment not only disrupts the localization of Kif26b to microtubules but also promotes phosphorylation and polyubiquitination of Kif26b. These results suggest that the function of Kif26b is microtubule-based and that Kif26b degradation in the metanephric mesenchyme via the ubiquitin-proteasome pathway may be important for proper kidney development.
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Affiliation(s)
- Takeshi Terabayashi
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- The Global COE “Cell Fate Regulation Research and Education Unit,” Kumamoto University, Honjo, Kumamoto, Japan
| | - Masaji Sakaguchi
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- The Global COE “Cell Fate Regulation Research and Education Unit,” Kumamoto University, Honjo, Kumamoto, Japan
| | - Kaori Shinmyozu
- Proteomics Laboratory, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
| | - Toshio Ohshima
- Department of Life Science and Medical Bio-Science, Waseda University, Tokyo, Japan
| | - Ai Johjima
- The Global COE “Cell Fate Regulation Research and Education Unit,” Kumamoto University, Honjo, Kumamoto, Japan
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Teru Ogura
- The Global COE “Cell Fate Regulation Research and Education Unit,” Kumamoto University, Honjo, Kumamoto, Japan
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- The Global COE “Cell Fate Regulation Research and Education Unit,” Kumamoto University, Honjo, Kumamoto, Japan
- * E-mail:
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27
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Ezrin ubiquitylation by the E3 ubiquitin ligase, WWP1, and consequent regulation of hepatocyte growth factor receptor activity. PLoS One 2012; 7:e37490. [PMID: 22629406 PMCID: PMC3358263 DOI: 10.1371/journal.pone.0037490] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/20/2012] [Indexed: 12/31/2022] Open
Abstract
The membrane cytoskeleton linker ezrin participates in several functions downstream of the receptor Met in response to Hepatocyte Growth Factor (HGF) stimulation. Here we report a novel interaction of ezrin with a HECT E3 ubiquitin ligase, WWP1/Aip5/Tiul1, a potential oncogene that undergoes genomic amplification and overexpression in human breast and prostate cancers. We show that ezrin binds to the WW domains of WWP1 via the consensus motif PPVY477 present in ezrin’s C-terminus. This association results in the ubiquitylation of ezrin, a process that requires an intact PPVY477 motif. Interestingly ezrin ubiquitylation does not target the protein for degradation by the proteasome. We find that ezrin ubiquitylation by WWP1 in epithelial cells leads to the upregulation of Met level in absence of HGF stimulation and increases the response of Met to HGF stimulation as measured by the ability of the cells to heal a wound. Interestingly this effect requires ubiquitylated ezrin since it can be rescued, after depletion of endogenous ezrin, by wild type ezrin but not by a mutant of ezrin that cannot be ubiquitylated. Taken together our data reveal a new role for ezrin in Met receptor stability and activity through its association with the E3 ubiquitin ligase WWP1. Given the role of Met in cell proliferation and tumorigenesis, our results may provide a mechanistic basis for understanding the role of ezrin in tumor progression.
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Muñoz-Soriano V, Nieto-Arellano R, Paricio N. Septin 4, the drosophila ortholog of human CDCrel-1, accumulates in parkin mutant brains and is functionally related to the Nedd4 E3 ubiquitin ligase. J Mol Neurosci 2012; 48:136-43. [PMID: 22562816 DOI: 10.1007/s12031-012-9788-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/24/2012] [Indexed: 11/26/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder. Although most PD cases are sporadic, several loci have been involved in the disease. parkin (PARK) is causative of autosomal recessive juvenile Parkinsonism (ARJP) and encodes an E3 ubiquitin ligase associated with proteasomal degradation. It was proposed that loss of PARK function may lead to the toxic accumulation of its substrates in the brain, thus causing dopaminergic (DA) neuron death. Indeed, the first identified PARK substrate was CDCrel-1, a protein of the Septin family that accumulates in ARPJ brains. Drosophila has been used as a successful model organism to study PD broadly contributing to the understanding of the disease. Consistently, park mutant flies recapitulate some key features of ARJP patients. In this scenario, we previously reported that overexpression of Septin 4 (Sep4), the Drosophila ortholog of CDCrel-1, is toxic for DA neurons and interacts physically with Park, thus suggesting that Sep4 could be a Park substrate in Drosophila. Confirming this hypothesis, we show that Sep4 accumulates in park mutant brains as its human counterpart. Furthermore, we demonstrate that Nedd4, another E3 ubiquitin ligase that may have a role in PD, is functionally related to Sep4 and could be involved in regulating Sep4 subcellular localization/trafficking.
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Affiliation(s)
- Verónica Muñoz-Soriano
- Departamento de Genética, Facultad de CC Biológicas, Universidad de Valencia, Dr. Moliner 50, Burjassot, 46100, Valencia, Spain
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29
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Skouloudaki K, Walz G. YAP1 recruits c-Abl to protect angiomotin-like 1 from Nedd4-mediated degradation. PLoS One 2012; 7:e35735. [PMID: 22558212 PMCID: PMC3338797 DOI: 10.1371/journal.pone.0035735] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/21/2012] [Indexed: 11/29/2022] Open
Abstract
Background Tissue development and organ growth require constant remodeling of cell-cell contacts formed between epithelial cells. The Hippo signaling cascade curtails organ growth by excluding the transcriptional co-activator Yes Associated Protein 1 (YAP1) from the nucleus. Angiomotin family members recruit YAP1 to tight junctions [1], but whether YAP1 plays a specific role outside of the nucleus is currently unknown. Methodology/Principal Findings The present study demonstrates that the E3 ubiquitin ligase Nedd4.2 targets Angiomotin-like 1 (AMOTL1), a family member that promotes the formation of epithelial tight junctions, for ubiquitin-dependent degradation. Unexpectedly, YAP1 antagonizes the function of Nedd4.2, and protects AMOTL1 against Nedd4.2-mediated degradation. YAP1 recruits c-Abl, a tyrosine kinase that binds and phosphorylates Nedd4.2 on tyrosine residues, thereby modifying its ubiquitin-ligase activity. Conclusions/Significance Our results uncover a novel function for cytoplasmic YAP1. YAP1 recruits c-Abl to protect AMOTL1 against Nedd4.2-mediated degradation. Thus, YAP1, excluded from the nucleus, contributes to the maintenance of tight junctions.
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Affiliation(s)
| | - Gerd Walz
- Renal Division, University Hospital Freiburg, Freiburg, Germany
- Center for Biological Signaling Studies (bioss), Freiburg, Germany
- * E-mail:
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30
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Soond SM, Chantry A. How ubiquitination regulates the TGF-β signalling pathway: new insights and new players: new isoforms of ubiquitin-activating enzymes in the E1-E3 families join the game. Bioessays 2012; 33:749-58. [PMID: 21932223 DOI: 10.1002/bies.201100057] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ubiquitination of protein species in regulating signal transduction pathways is universally accepted as of fundamental importance for normal development, and defects in this process have been implicated in the progression of many human diseases. One pathway that has received much attention in this context is transforming growth factor-beta (TGF-β) signalling, particularly during the regulation of epithelial-mesenchymal transition (EMT) and tumour progression. While E3-ubiquitin ligases offer themselves as potential therapeutic targets, much remains to be unveiled regarding mechanisms that culminate in their regulation. With this in mind, the focus of this review highlights the regulation of the ubiquitination pathway and the significance of a recently described group of NEDD4 E3-ubiquitin ligase isoforms in the context of TGF-β pathway regulation. Moreover, we now broaden these observations to incorporate a growing number of protein isoforms within the ubiquitin ligase superfamily as a whole, and discuss their relevance in defining a new 'iso-ubiquitinome'.
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Affiliation(s)
- Surinder M Soond
- University of East Anglia, School Of Biological Sciences, Norwich, Norfolk, UK.
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31
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Ng SK, Tan SH. DISCOVERING PROTEIN–PROTEIN INTERACTIONS. J Bioinform Comput Biol 2011; 1:711-41. [PMID: 15290761 DOI: 10.1142/s0219720004000600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 12/12/2003] [Accepted: 12/13/2003] [Indexed: 11/18/2022]
Abstract
The ongoing genomics and proteomics efforts have helped identify many new genes and proteins in living organisms. However, simply knowing the existence of genes and proteins does not tell us much about the biological processes in which they participate. Many major biological processes are controlled by protein interaction networks. A comprehensive description of protein–protein interactions is therefore necessary to understand the genetic program of life. In this tutorial, we provide an overview of the various current high-throughput methods for discovering protein–protein interactions, covering both the conventional experimental methods and new computational approaches.
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Affiliation(s)
- See-Kiong Ng
- Knowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore.
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32
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Zhong Y, Shtineman-Kotler A, Nguyen L, Iliadi KG, Boulianne GL, Rotin D. A splice isoform of DNedd4, DNedd4-long, negatively regulates neuromuscular synaptogenesis and viability in Drosophila. PLoS One 2011; 6:e27007. [PMID: 22110599 PMCID: PMC3215714 DOI: 10.1371/journal.pone.0027007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 10/07/2011] [Indexed: 11/29/2022] Open
Abstract
Background Neuromuscular (NM) synaptogenesis is a tightly regulated process. We previously showed that in flies, Drosophila Nedd4 (dNedd4/dNedd4S) is required for proper NM synaptogenesis by promoting endocytosis of commissureless from the muscle surface, a pre-requisite step for muscle innervation. DNedd4 is an E3 ubiquitin ligase comprised of a C2-WW(x3)-Hect domain architecture, which includes several splice isoforms, the most prominent ones are dNedd4-short (dNedd4S) and dNedd4-long (dNedd4Lo). Methodology/Principal Findings We show here that while dNedd4S is essential for NM synaptogenesis, the dNedd4Lo isoform inhibits this process and causes lethality. Our results reveal that unlike dNedd4S, dNedd4Lo cannot rescue the lethality of dNedd4 null (DNedd4T121FS) flies. Moreover, overexpression of UAS-dNedd4Lo specifically in wildtype muscles leads to NM synaptogenesis defects, impaired locomotion and larval lethality. These negative effects of dNedd4Lo are ameliorated by deletion of two regions (N-terminus and Middle region) unique to this isoform, and by inactivating the catalytic activity of dNedd4Lo, suggesting that these unique regions, as well as catalytic activity, are responsible for the inhibitory effects of dNedd4Lo on synaptogenesis. In accord with these findings, we demonstrate by sqRT-PCR an increase in dNedd4S expression relative to the expression of dNedd4Lo during embryonic stages when synaptogenesis takes place. Conclusion/Significance Our studies demonstrate that splice isoforms of the same dNedd4 gene can lead to opposite effects on NM synaptogenesis.
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Affiliation(s)
- Yunan Zhong
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Alina Shtineman-Kotler
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Leo Nguyen
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Konstantin G. Iliadi
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gabrielle L. Boulianne
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Daniela Rotin
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- * E-mail:
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33
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Morishima N, Nakanishi K, Nakano A. Activating transcription factor-6 (ATF6) mediates apoptosis with reduction of myeloid cell leukemia sequence 1 (Mcl-1) protein via induction of WW domain binding protein 1. J Biol Chem 2011; 286:35227-35. [PMID: 21841196 PMCID: PMC3186435 DOI: 10.1074/jbc.m111.233502] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 08/09/2011] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is involved in both physiological and pathological apoptosis. ER stress triggers the unfolded protein response (UPR), which can then initiate apoptosis, when the cell fails to restore ER homeostasis. However, the mechanism employed by the UPR to lead cells into apoptosis is unknown. Among the three proximal sensors of ER stress, activating transcription factor-6 (ATF6) is specifically activated in apoptotic myoblasts during myoblast differentiation. This implies that active ATF6 has the ability to mediate apoptosis. Here, we demonstrate that overexpression of active ATF6 induced apoptosis in myoblast cells. Moreover, coexpression of a dominant negative form of ATF6 suppressed apoptosis. This suggested that apoptosis-related pathways depended on ATF6-mediated transcription activation. ATF6 caused up-regulation of the WBP1 (WW domain binding protein 1), probably via an indirect mechanism. Furthermore, WBP1 was also found to be proapoptotic. The silencing of WBP1 with small hairpin RNAs caused partial, but significant suppression of ATF6-induced apoptosis. Overexpression of active ATF6 or WBP1 caused a specific reduction in an anti-apoptotic protein, Mcl-1 (myeloid cell leukemia sequence 1). This suggested a molecular link between the UPR and an apoptosis regulator. Neither Bcl-2 nor Bcl-x(L) were reduced upon apoptosis induction in C2C12 cells that overexpressed ATF6 or WBP1. Cells treated with ER stressors underwent apoptosis concomitant with an up-regulation of WBP1 and suppression of Mcl-1. These results suggested that Mcl-1 is a determinant of cell fate, and ATF6 mediates apoptosis via specific suppression of Mcl-1 through up-regulation of WBP1.
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Affiliation(s)
- Nobuhiro Morishima
- Molecular Membrane Biology Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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34
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Abstract
Most membrane-enveloped viruses bud from infected cells by hijacking the host ESCRT machinery. The ESCRTs are recruited to the budding sites by viral proteins that contain short proline (Pro)-rich motifs (PRMs) known as late domains. The late domains probably evolved by co-opting host PRMs involved in the normal functions of ESCRTs in endosomal sorting and cytokinesis. The solution and crystal structures of PRMs bound to their interaction partners explain the conserved roles of Pro and other residues that predominate in these sequences. PRMs are often grouped together in much larger Pro-rich regions (PRRs) of as many as 150 residues. The PRR of the ESCRT-associated protein, ALIX, autoregulates its conformation and activity. The robustness of different viral budding and host pathways to impairments in Pro-based interactions varies considerably. The known biology of PRM recognition in the ESCRT pathway seems, in principle, compatible with antiviral development, given our increasingly nuanced understanding of the relative weakness and robustness of the host and viral processes.
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Affiliation(s)
- Xuefeng Ren
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James H. Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Espanel X, Navin N, Kato Y, Tanokura M, Sudol M. Probing WW Domains to Uncover and Refine Determinants of Specificity in Ligand Recognition. Cytotechnology 2011; 43:105-11. [PMID: 19003214 PMCID: PMC3449593 DOI: 10.1023/b:cyto.0000039913.56708.06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the specificity of protein-protein interaction mediated by domains and their ligands will have strong impact on basic and applied research. Visual inspection of WW domain sequences prompted a general classification of the domains into two large subfamilies. One subfamily contains two consecutive aromatic residues in the beta 2 strand of the domain whereas the other contains three or four consecutive aromatic residues in the same position. In the recent past, we proposed a rule of 'two vs. three aromatics' in the beta 2 strand of WW domains as a molecular discriminator between Class I and Class II WW domains, which recognize PPxY or PPLP motifs, respectively. Using phage display libraries expressing WW domains with random sequences replacing a part of the beta 2 strand, we provided additional evidence supporting our rule. We conclude that three consecutive aromatic amino acids within the beta 2 strand of WW domain are required but not always sufficient for the WW domain to belong to Class II.
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Affiliation(s)
- X Espanel
- Sanofi-Synthelabo, Labege Innopole Voie 1, 31676, Labege, France
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36
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Rapali P, Radnai L, Süveges D, Harmat V, Tölgyesi F, Wahlgren WY, Katona G, Nyitray L, Pál G. Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PLoS One 2011; 6:e18818. [PMID: 21533121 PMCID: PMC3078936 DOI: 10.1371/journal.pone.0018818] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/10/2011] [Indexed: 11/27/2022] Open
Abstract
LC8 dynein light chain (DYNLL) is a eukaryotic hub protein that is thought to function as a dimerization engine. Its interacting partners are involved in a wide range of cellular functions. In its dozens of hitherto identified binding partners DYNLL binds to a linear peptide segment. The known segments define a loosely characterized binding motif: [D/S]-4K-3X-2[T/V/I]-1Q0[T/V]1[D/E]2. The motifs are localized in disordered segments of the DYNLL-binding proteins and are often flanked by coiled coil or other potential dimerization domains. Based on a directed evolution approach, here we provide the first quantitative characterization of the binding preference of the DYNLL binding site. We displayed on M13 phage a naïve peptide library with seven fully randomized positions around a fixed, naturally conserved glutamine. The peptides were presented in a bivalent manner fused to a leucine zipper mimicking the natural dimer to dimer binding stoichiometry of DYNLL-partner complexes. The phage-selected consensus sequence V-5S-4R-3G-2T-1Q0T1E2 resembles the natural one, but is extended by an additional N-terminal valine, which increases the affinity of the monomeric peptide twentyfold. Leu-zipper dimerization increases the affinity into the subnanomolar range. By comparing crystal structures of an SRGTQTE-DYNLL and a dimeric VSRGTQTE-DYNLL complex we find that the affinity enhancing valine is accommodated in a binding pocket on DYNLL. Based on the in vitro evolved sequence pattern we predict a large number of novel DYNLL binding partners in the human proteome. Among these EML3, a microtubule-binding protein involved in mitosis contains an exact match of the phage-evolved consensus and binds to DYNLL with nanomolar affinity. These results significantly widen the scope of the human interactome around DYNLL and will certainly shed more light on the biological functions and organizing role of DYNLL in the human and other eukaryotic interactomes.
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Affiliation(s)
- Péter Rapali
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - László Radnai
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Dániel Süveges
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Veronika Harmat
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- Protein Modeling Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Tölgyesi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | | | - Gergely Katona
- Department of Chemistry, University of Gothenburg, Gothenburg, Sweden
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail: (LN); (GP)
| | - Gábor Pál
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail: (LN); (GP)
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Sunbul M, Emerson N, Yin J. Enzyme-catalyzed substrate attachment to phage surfaces for the selection of catalytic activities. Chembiochem 2011; 12:380-6. [PMID: 21290537 DOI: 10.1002/cbic.201000475] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Murat Sunbul
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, GCIS E505, Chicago, IL 60637, USA
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38
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Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S. High-resolution mapping of protein sequence-function relationships. Nat Methods 2010; 7:741-6. [PMID: 20711194 PMCID: PMC2938879 DOI: 10.1038/nmeth.1492] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/13/2010] [Indexed: 12/30/2022]
Abstract
We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity and high-throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position had unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence.
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Affiliation(s)
- Douglas M. Fowler
- Department of Genome Sciences University of Washington Box 355065 Seattle, WA 98195
| | - Carlos L. Araya
- Department of Genome Sciences University of Washington Box 355065 Seattle, WA 98195
| | - Sarel J. Fleishman
- Department of Biochemistry University of Washington Box 355065 Seattle, WA 98195
| | - Elizabeth H. Kellogg
- Department of Biochemistry University of Washington Box 355065 Seattle, WA 98195
| | - Jason J. Stephany
- Department of Genome Sciences University of Washington Box 355065 Seattle, WA 98195
- Howard Hughes Medical Institute
| | - David Baker
- Department of Biochemistry University of Washington Box 355065 Seattle, WA 98195
- Howard Hughes Medical Institute
| | - Stanley Fields
- Department of Genome Sciences University of Washington Box 355065 Seattle, WA 98195
- Department of Medicine University of Washington Box 355065 Seattle, WA 98195
- Howard Hughes Medical Institute
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Abstract
The homologous to the E6-associated protein carboxyl terminus (HECT) domain E3 ubiquitin ligase Smurf1 is the first E3 ligase to be implicated in regulating bone cell function. The involvement of Smurf1 in multiple signaling pathways and pathological conditions is presently an area of extensive scientific interest. This review highlights recent works exploring Smurf-regulated biological processes in bone cells and highlights recent discoveries surrounding the regulatory mechanisms modulating its catalytic activity and substrate recognition capability. Moreover, we discuss the relevance of targeting the HECT E3s through the development of small-molecule inhibitors as an anticancer therapeutic strategy.
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Affiliation(s)
- Lianping Xing
- Department of Pathology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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40
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Fouladkou F, Lu C, Jiang C, Zhou L, She Y, Walls JR, Kawabe H, Brose N, Henkelman RM, Huang A, Bruneau BG, Rotin D. The ubiquitin ligase Nedd4-1 is required for heart development and is a suppressor of thrombospondin-1. J Biol Chem 2009; 285:6770-80. [PMID: 20026598 DOI: 10.1074/jbc.m109.082347] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nedd4 (Nedd4-1) is a Hect domain E3 ubiquitin ligase that also contains a C2 domain and three WW domains. Despite numerous in vitro studies, its biological function in vivo is not well understood. Here we show that disruption of Nedd4-1 in mice (leaving Nedd4-2 intact) caused embryonic lethality at mid gestation, with pronounced heart defects (double-outlet right ventricle and atrioventricular cushion defects) and vasculature abnormalities. Quantitative mass spectrometry and immunoblot analyses of lysates from the wild type and knock-out mouse embryonic fibroblasts to identify Nedd4-1 in vivo targets revealed dramatically increased amounts of thrombospondin-1 (Tsp-1) in the knock-out mouse embryonic fibroblasts and embryos. Tsp-1 is an inhibitor of angiogenesis, and its elevated level was mediated primarily by enhanced transcription. Interestingly, the administration of aspirin (an inhibitor of Tsp-1) to the pregnant heterozygote mothers led to a reduction in Tsp-1 levels and a substantial rescue of the embryonic lethality. These results suggest that Nedd4-1 is a suppressor of Tsp1 and that increased levels of Tsp-1 in the Nedd4-1 knock-out mice may have contributed to the developmental defect observed in the embryos.
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Affiliation(s)
- Fatemeh Fouladkou
- Program in Cell Biology and the Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
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41
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Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Mol Syst Biol 2009; 5:333. [PMID: 19953087 PMCID: PMC2824488 DOI: 10.1038/msb.2009.85] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 10/06/2009] [Indexed: 12/18/2022] Open
Abstract
Target recognition by the ubiquitin system is mediated by E3 ubiquitin ligases. Nedd4 family members are E3 ligases comprised of a C2 domain, 2–4 WW domains that bind PY motifs (L/PPxY) and a ubiquitin ligase HECT domain. The nine Nedd4 family proteins in mammals include two close relatives: Nedd4 (Nedd4-1) and Nedd4L (Nedd4-2), but their global substrate recognition or differences in substrate specificity are unknown. We performed in vitro ubiquitylation and binding assays of human Nedd4-1 and Nedd4-2, and rat-Nedd4-1, using protein microarrays spotted with ∼8200 human proteins. Top hits (substrates) for the ubiquitylation and binding assays mostly contain PY motifs. Although several substrates were recognized by both Nedd4-1 and Nedd4-2, others were specific to only one, with several Tyr kinases preferred by Nedd4-1 and some ion channels by Nedd4-2; this was subsequently validated in vivo. Accordingly, Nedd4-1 knockdown or knockout in cells led to sustained signalling via some of its substrate Tyr kinases (e.g. FGFR), suggesting Nedd4-1 suppresses their signalling. These results demonstrate the feasibility of identifying substrates and deciphering substrate specificity of mammalian E3 ligases.
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42
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Lee JRE, Oestreich AJ, Payne JA, Gunawan MS, Norgan AP, Katzmann DJ. The HECT domain of the ubiquitin ligase Rsp5 contributes to substrate recognition. J Biol Chem 2009; 284:32126-37. [PMID: 19744925 DOI: 10.1074/jbc.m109.048629] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ubiquitin modification of endosomal membrane proteins is a signal for active inclusion into the Multivesicular Body (MVB) pathway, resulting in lysosomal degradation. However, the endosome represents a dynamic site of protein sorting with a majority of proteins destined for recycling, rather than MVB targeting. Substrate recognition by ubiquitin ligases is therefore highly regulated. We have investigated substrate recognition by the Nedd4 ortholog Rsp5 as a model for understanding ligase-substrate interactions. Rsp5 interacts directly with its substrate Cps1 via a novel interaction mode. Perturbation of this mode of interaction revealed a compensatory role for the Rsp5 adaptor Bsd2. These results highlight the ability of Rsp5 to interact with substrates via multiple modalities, suggesting additional mechanisms of regulating this interaction and relevant outcomes.
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Affiliation(s)
- Jacqueline R E Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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Fontana JR, Posakony JW. Both inhibition and activation of Notch signaling rely on a conserved Neuralized-binding motif in Bearded proteins and the Notch ligand Delta. Dev Biol 2009; 333:373-85. [PMID: 19580805 DOI: 10.1016/j.ydbio.2009.06.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/20/2009] [Accepted: 06/27/2009] [Indexed: 11/16/2022]
Abstract
Lateral inhibition is one of the key functions of Notch signaling during animal development. In the proneural clusters that give rise to Drosophila mechanosensory bristles, Delta (Dl) ligand in the sensory organ precursor (SOP) cell is targeted for ubiquitination by the E3 ligase Neuralized (Neur), resulting in activation of Dl's capacity to signal to the Notch receptor on neighboring cells. The cells that receive this signal activate a genetic program that suppresses their SOP fate potential, insuring that only a single SOP develops within each cluster. Using multiple lines of investigation, we provide evidence that members of the Bearded family of proteins (BFMs) inhibit Dl activation in non-SOP cells by binding to Neur and preventing it from interacting with Dl. We show that this activity of BFMs is dependent on the conserved NXXN motif, and report the unexpected finding that several BFMs include multiple functional copies of this motif. We find that a conserved NXXN motif in the intracellular domain of Dl is responsible for its interaction with Neur, indicating direct competition between Dl and BFMs for binding to Neur, and we show that Neur-dependent endocytosis of Dl requires the integrity of its NXXN motif. Our results illuminate the mechanism of an important regulatory event in Notch signaling that appears to be conserved between insects and crustaceans.
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Affiliation(s)
- Joseph R Fontana
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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44
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Bhandari D, Robia SL, Marchese A. The E3 ubiquitin ligase atrophin interacting protein 4 binds directly to the chemokine receptor CXCR4 via a novel WW domain-mediated interaction. Mol Biol Cell 2008; 20:1324-39. [PMID: 19116316 DOI: 10.1091/mbc.e08-03-0308] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The E3 ubiquitin ligase atrophin interacting protein 4 (AIP4) mediates ubiquitination and down-regulation of the chemokine receptor CXCR4. AIP4 belongs to the Nedd4-like homologous to E6-AP carboxy terminus domain family of E3 ubiquitin ligases, which typically bind proline-rich motifs within target proteins via the WW domains. The intracellular domains of CXCR4 lack canonical WW domain binding motifs; thus, whether AIP4 is targeted to CXCR4 directly or indirectly via an adaptor protein remains unknown. Here, we show that AIP4 can interact directly with CXCR4 via a novel noncanonical WW domain-mediated interaction involving serine residues 324 and 325 within the carboxy-terminal tail of CXCR4. These serine residues are critical for mediating agonist-promoted binding of AIP4 and subsequent ubiquitination and degradation of CXCR4. These residues are phosphorylated upon agonist activation and phosphomimetic mutants show enhanced binding to AIP4, suggesting a mechanism whereby phosphorylation mediates the interaction between CXCR4 and AIP4. Our data reveal a novel noncanonical WW domain-mediated interaction involving phosphorylated serine residues in the absence of any proline residues and suggest a novel mechanism whereby an E3 ubiquitin ligase is targeted directly to an activated G protein-coupled receptor.
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Affiliation(s)
- Deepali Bhandari
- Program in Molecular Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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45
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Nguyen Huu NS, Ryder WDJ, Zeps N, Flasza M, Chiu M, Hanby AM, Poulsom R, Clarke RB, Baron M. Tumour-promoting activity of altered WWP1 expression in breast cancer and its utility as a prognostic indicator. J Pathol 2008; 216:93-102. [PMID: 18604872 DOI: 10.1002/path.2385] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
WWP1 is a ubiquitin ligase, associated with the post-translational regulation of several tumour-promoting and tumour suppressor proteins. Here we show that WWP1 expression is up-regulated in a subset of breast tumour cell lines and primary breast tumours. We overexpressed WWP1 in MCF10A breast epithelial cells and demonstrated increased cell growth and anchorage-independent colony formation. RNAi knockdown of WWP1 expression in T47D and MCF7 breast tumour cell lines reduced anchorage-independent colony formation. We used WWP1 protein expression levels, in combination with its sub-cellular localization, to classify breast tumours into four categories. Surprisingly, a category with low/absent WWP1 expression displayed a consistently worse prognosis compared with WWP1-expressing tumours. Importantly, the association with disease-free survival was independent of the status of other commonly used prognostic indicators. Thus, WWP1 is a prognostic marker and may be a potential therapeutic target for a subset of breast tumours.
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Affiliation(s)
- N S Nguyen Huu
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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46
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Regulation of Nedd4-2 self-ubiquitination and stability by a PY motif located within its HECT-domain. Biochem J 2008; 415:155-63. [DOI: 10.1042/bj20071708] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ubiquitin ligases play a pivotal role in substrate recognition and ubiquitin transfer, yet little is known about the regulation of their catalytic activity. Nedd4 (neural-precursor-cell-expressed, developmentally down-regulated 4)-2 is an E3 ubiquitin ligase composed of a C2 domain, four WW domains (protein–protein interaction domains containing two conserved tryptophan residues) that bind PY motifs (L/PPXY) and a ubiquitin ligase HECT (homologous with E6-associated protein C-terminus) domain. In the present paper we show that the WW domains of Nedd4-2 bind (weakly) to a PY motif (LPXY) located within its own HECT domain and inhibit auto-ubiquitination. Pulse–chase experiments demonstrated that mutation of the HECT PY-motif decreases the stability of Nedd4-2, suggesting that it is involved in stabilization of this E3 ligase. Interestingly, the HECT PY-motif mutation does not affect ubiquitination or down-regulation of a known Nedd4-2 substrate, ENaC (epithelial sodium channel). ENaC ubiquitination, in turn, appears to promote Nedd4-2 self-ubiquitination. These results support a model in which the inter- or intra-molecular WW-domain–HECT PY-motif interaction stabilizes Nedd4-2 by preventing self-ubiquitination. Substrate binding disrupts this interaction, allowing self-ubiquitination of Nedd4-2 and subsequent degradation, resulting in down-regulation of Nedd4-2 once it has ubiquitinated its target. These findings also point to a novel mechanism employed by a ubiquitin ligase to regulate itself differentially compared with substrate ubiquitination and stability.
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47
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The ubiquitin ligase Nedd4-1 is dispensable for the regulation of PTEN stability and localization. Proc Natl Acad Sci U S A 2008; 105:8585-90. [PMID: 18562292 DOI: 10.1073/pnas.0803233105] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PTEN is a tumor suppressor frequently mutated in cancer. Recent reports implicated Nedd4-1 as the E3 ubiquitin ligase for PTEN that regulates its stability and nuclear localization. We tested the physiological role of Nedd4-1 as a PTEN regulator by using cells and tissues derived from two independently generated strains of mice with their Nedd4-1 gene disrupted. PTEN stability and ubiquitination were indistinguishable between the wild-type and Nedd4-1-deficient cells, and an interaction between the two proteins could not be detected. Moreover, PTEN subcellular distribution, showing prominent cytoplasmic and nuclear staining, was independent of Nedd4-1 presence. Finally, activation of PKB/Akt, a major downstream target of cytoplasmic PTEN activity, and the ability of PTEN to transactivate the Rad51 promoter, a measure of its nuclear function, were unaffected by the loss of Nedd4-1. Taken together, our results fail to support a role for Nedd4-1 as the E3 ligase regulating PTEN stability and subcellular localization.
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48
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Jennings MD, Blankley RT, Baron M, Golovanov AP, Avis JM. Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex. J Biol Chem 2007; 282:29032-29042. [PMID: 17656366 PMCID: PMC4244684 DOI: 10.1074/jbc.m703453200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WW domains target proline-tyrosine (PY) motifs and frequently function as tandem pairs. When studied in isolation, single WW domains are notably promiscuous and regulatory mechanisms are undoubtedly required to ensure selective interactions. Here, we show that the fourth WW domain (WW4) of Suppressor of Deltex, a modular Nedd4-like protein that down-regulates the Notch receptor, is the primary mediator of a direct interaction with a Notch-PY motif. A natural Trp to Phe substitution in WW4 reduces its affinity for general PY sequences and enhances selective interaction with the Notch-PY motif via compensatory specificity-determining interactions with PY-flanking residues. When WW4 is paired with WW3, domain-domain association, impeding proper folding, competes with Notch-PY binding to WW4. This novel mode of autoinhibition is relieved by binding of another ligand to WW3. Such cooperativity may facilitate the transient regulatory interactions observed in vivo between Su(dx) and Notch in the endocytic pathway. The highly conserved tandem arrangement of WW domains in Nedd4 proteins, and similar arrangements in more diverse proteins, suggests domain-domain communication may be integral to regulation of their associated cellular activities.
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Affiliation(s)
- Martin D Jennings
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN
| | - Richard T Blankley
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN
| | - Martin Baron
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester M13 9PT, United Kingdom.
| | - Alexander P Golovanov
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN.
| | - Johanna M Avis
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN.
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Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D. Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol 2007; 3:116. [PMID: 17551511 PMCID: PMC1911201 DOI: 10.1038/msb4100159] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 04/24/2007] [Indexed: 01/25/2023] Open
Abstract
Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.
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Affiliation(s)
- Ronish Gupta
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bart Kus
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Fladd
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James Wasmuth
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raffi Tonikian
- Banting & Best Department of Medical Research, University of Toronto, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev Sidhu
- Department of Protein Engineering, Genentech, South San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA, USA
| | - John Parkinson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniela Rotin
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8. Tel.: +1 416-813-5098; Fax: +1 416-813-8456;
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50
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Tonikian R, Zhang Y, Boone C, Sidhu SS. Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protoc 2007; 2:1368-86. [PMID: 17545975 DOI: 10.1038/nprot.2007.151] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signaling complexes usually involve multidomain proteins containing catalytic domains and peptide recognition modules (PRMs), which mediate protein-protein interactions and assemble complexes by binding to ligands containing a core sequence motif. Concomitant to large-scale physical interaction screening, considerable effort has been devoted toward the elucidation of consensus profiles for common PRMs. We describe herein a robust and proven protocol to generate consensus profiles for PRMs using phage-displayed peptide libraries. The initial phase of the protocol entails the cloning, expression and purification of PRMs as fusion proteins, in addition to the construction of highly diverse phage-displayed peptide libraries. The affinity selection process described thereafter enables a single researcher to efficiently probe the recognition profiles of numerous PRMs in a 1 week time period.
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Affiliation(s)
- Raffi Tonikian
- Department of Molecular and Medical Genetics, University of Toronto, #4398 Medical Sciences Building, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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