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Rotin D, Prag G. Physiological Functions of the Ubiquitin Ligases Nedd4-1 and Nedd4-2. Physiology (Bethesda) 2024; 39:18-29. [PMID: 37962894 DOI: 10.1152/physiol.00023.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/15/2023] Open
Abstract
The Nedd4 family of E3 ubiquitin ligases, consisting of a C2-WW(n)-HECT domain architecture, includes the closely related Nedd4/Nedd4-1 and Nedd4L/Nedd4-2, which play critical roles in human physiology and pathophysiology.This review focuses on the regulation of enzymatic activity of these Nedd4 proteins, as well as on their roles in regulating stability and function of membrane and other signaling proteins, such as ion channels, ion transporters, and growth factor receptors. The diseases caused by impairment of such regulation are discussed, as well as opportunities and challenges for targeting these enzymes for therapy.
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Affiliation(s)
- Daniela Rotin
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Biochemistry Department, University of Toronto, Ontario, Canada
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
- Sagol School of Neuroscience, Tel Aviv University, Israel
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2
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Kefalas G, Rotin D. Primate-specific isoform of Nedd4-1 regulates substrate binding via Ser/Thr phosphorylation and 14-3-3 binding. Sci Rep 2023; 13:17903. [PMID: 37863970 PMCID: PMC10589272 DOI: 10.1038/s41598-023-44761-9] [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: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
Nedd4 (Nedd4-1) is an E3 ubiquitin ligase involved in crucial biological processes such as growth factor receptor signaling. While canonical Nedd4-1 comprises a C2-WW(4)-HECT domain architecture, alternative splicing produces non-canonical isoforms that are poorly characterized. Here we characterized Nedd4-1(NE), a primate-specific isoform of Nedd4-1 that contains a large N-terminal Extension (NE) that replaces most of the C2 domain. We show that Nedd4-1(NE) mRNA is ubiquitously expressed in human tissues and cell lines. Moreover, we found that Nedd4-1(NE) is more active than the canonical Nedd4-1 isoform, likely due to the absence of a C2 domain-mediated autoinhibitory mechanism. Additionally, we identified two Thr/Ser phosphoresidues in the NE region that act as binding sites for 14-3-3 proteins, and show that phosphorylation on these sites reduces substrate binding. Finally, we show that the NE region can act as a binding site for the RPB2 subunit of RNA polymerase II, a unique substrate of Nedd4-1(NE) but not the canonical Nedd4-1. Taken together, our results demonstrate that alternative splicing of the ubiquitin ligase Nedd4-1 can produce isoforms that differ in their catalytic activity, binding partners and substrates, and mechanisms of regulation.
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Affiliation(s)
- George Kefalas
- Cell Biology Program, the Hospital for Sick Children, PGCRL 19-9715, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Biochemistry Department, University of Toronto, Toronto, ON, M5G 0A4, Canada
| | - Daniela Rotin
- Cell Biology Program, the Hospital for Sick Children, PGCRL 19-9715, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Biochemistry Department, University of Toronto, Toronto, ON, M5G 0A4, Canada.
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Xu D, Zhu W, Wu Y, Wei S, Shu G, Tian Y, Du X, Tang J, Feng Y, Wu G, Han X, Zhao X. Whole-genome sequencing revealed genetic diversity, structure and patterns of selection in Guizhou indigenous chickens. BMC Genomics 2023; 24:570. [PMID: 37749517 PMCID: PMC10521574 DOI: 10.1186/s12864-023-09621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The eight phenotypically distinguishable indigenous chicken breeds in Guizhou province of China are great resources for high-quality development of the poultry industry in China. However, their full value and potential have yet to be understood in depth. To illustrate the genetic diversity, the relationship and population structure, and the genetic variation patterns shaped by selection in Guizhou indigenous chickens, we performed a genome-wide analysis of 240 chickens from 8 phenotypically and geographically representative Guizhou chicken breeds and 60 chickens from 2 commercial chicken breeds (one broiler and one layer), together with 10 red jungle fowls (RJF) genomes available from previous studies. RESULTS The results obtained in this present study showed that Guizhou chicken breed populations harbored higher genetic diversity as compared to commercial chicken breeds, however unequal polymorphisms were present within Guizhou indigenous chicken breeds. The results from the population structure analysis markedly reflected the breeding history and the geographical distribution of Guizhou indigenous chickens, whereas, some breeds with complex genetic structure were ungrouped into one cluster. In addition, we confirmed mutual introgression within Guizhou indigenous chicken breeds and from commercial chicken breeds. Furthermore, selective sweep analysis revealed candidate genes which were associated with specific and common phenotypic characteristics evolved rapidly after domestication of Guizhou local chicken breeds and economic traits such as egg production performance, growth performance, and body size. CONCLUSION Taken together, the results obtained from the comprehensive analysis of the genetic diversity, genetic relationships and population structures in this study showed that Guizhou indigenous chicken breeds harbor great potential for commercial utilization, however effective conservation measures are currently needed. Additionally, the present study drew a genome-wide selection signature draft for eight Guizhou indigenous chicken breeds and two commercial breeds, as well as established a resource that can be exploited in chicken breeding programs to manipulate the genes associated with desired phenotypes. Therefore, this study will provide an essential genetic basis for further research, conservation, and breeding of Guizhou indigenous chickens.
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Affiliation(s)
- Dan Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Wei Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Youhao Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Shuo Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Gang Shu
- Department of Basic Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yaofu Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Xiaohui Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Jigao Tang
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Yulong Feng
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Gemin Wu
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Xue Han
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China.
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China.
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China.
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Yong D, Green SR, Ghiabi P, Santhakumar V, Vedadi M. Discovery of Nedd4 auto-ubiquitination inhibitors. Sci Rep 2023; 13:16057. [PMID: 37749144 PMCID: PMC10520017 DOI: 10.1038/s41598-023-42997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
E3 ubiquitin ligases are critical to the protein degradation pathway by catalyzing the final step in protein ubiquitination by mediating ubiquitin transfer from E2 enzymes to target proteins. Nedd4 is a HECT domain-containing E3 ubiquitin ligase with a wide range of protein targets, the dysregulation of which has been implicated in myriad pathologies, including cancer and Parkinson's disease. Towards the discovery of compounds disrupting the auto-ubiquitination activity of Nedd4, we developed and optimized a TR-FRET assay for high-throughput screening. Through selective screening of a library of potentially covalent compounds, compounds 25 and 81 demonstrated apparent IC50 values of 52 µM and 31 µM, respectively. Tandem mass spectrometry (MS/MS) analysis confirmed that 25 and 81 were covalently bound to Nedd4 cysteine residues (Cys182 and Cys867). In addition, 81 also adducted to Cys627. Auto-ubiquitination assays of Nedd4 mutants featuring alanine substitutions for each of these cysteines suggested that the mode of inhibition of these compounds occurs through blocking the catalytic Cys867. The discovery of these inhibitors could enable the development of therapeutics for various diseases caused by Nedd4 E3 ligase dysregulation.
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Affiliation(s)
- Darren Yong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Stuart R Green
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
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Cao L, Li H, Liu X, Wang Y, Zheng B, Xing C, Zhang N, Liu J. Expression and regulatory network of E3 ubiquitin ligase NEDD4 family in cancers. BMC Cancer 2023; 23:526. [PMID: 37291499 DOI: 10.1186/s12885-023-11007-w] [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: 12/06/2022] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
NEDD4 family represent an important group of E3 ligases, which regulate various cellular pathways of cell proliferation, cell junction and inflammation. Emerging evidence suggested that NEDD4 family members participate in the initiation and development of tumor. In this study, we systematically investigated the molecular alterations as well as the clinical relevance regarding NEDD4 family genes in 33 cancer types. Finally, we found that NEDD4 members showed increased expression in pancreas cancer and decreased expression in thyroid cancer. NEDD4 E3 ligase family genes had an average mutation frequency in the range of 0-32.1%, of which HECW1 and HECW2 demonstrated relatively high mutation rate. Breast cancer harbors large amount of NEDD4 copy number amplification. NEDD4 family members interacted proteins were enriched in various pathways including p53, Akt, apoptosis and autophagy, which were confirmed by further western blot and flow cytometric analysis in A549 and H1299 lung cancer cells. In addition, expression of NEDD4 family genes were associated with survival of cancer patients. Our findings provide novel insight into the effect of NEDD4 E3 ligase genes on cancer progression and treatment in the future.
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Affiliation(s)
- Liangzi Cao
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Hao Li
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Xiaofang Liu
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Yubang Wang
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Bowen Zheng
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Chengzhong Xing
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China.
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Jingwei Liu
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China.
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Wei J, Beebe-Dimmer J, Shi Z, Sample C, Yan G, Rifkin AS, Sadeghpour A, Gielzak M, Choi S, Moon D, Zheng SL, Helfand BT, Walsh PC, Xu J, Cooney KA, Isaacs WB. Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry. Prostate 2023; 83:454-461. [PMID: 36567534 DOI: 10.1002/pros.24477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Although men of African ancestry (AA) have the highest mortality rate from prostate cancer (PCa), relatively little is known about the germline variants that are associated with PCa risk in AA men. The goal of this study is to systematically evaluate rare, recurrent nonsynonymous variants across the exome for their association with PCa in AA men. METHODS Whole exome sequencing (WES) of germline DNA in two AA PCa patient cohorts of Johns Hopkins Hospital (N = 960) and Wayne State University (N = 747) was performed. All nonsynonymous variants present in both case cohorts, with a carrier rate between 0.5% and 1%, were identified. Their carrier rates were compared with rates from 8128 African/African American (AFR) control subjects from The Genome Aggregation Database (gnomAD) using Fisher's exact test. Significant variants, defined as false discovery rate (FDR) adjusted p-value ≤ 0.05, were further evaluated in AA PCa cases (N = 132) and controls (N = 1184) from the UK Biobank (UKB). RESULTS Two variants reached a pre-specified statistical significance level. The first was p.R14Q in GPRC5C (found in 0.47% of PCa cases and 0.01% of population controls); odds ratio (OR) for PCa was 37.46 (95% confidence interval CI 4.68-299.72), pexact = 7.01E-06, FDR-adjusted p-value = 0.05. The second was p.R511Q in IGF1R (found in 0.53% of PCa cases and 0.01% of population controls); OR for PCa was 21.54 (95%CI 4.65-99.76), pexact = 5.51E-06, FDR-adjusted p-value = 0.05. The mean percentage of African ancestry was similar between variant carriers and noncarriers of each variant, p > 0.05. In the UKB AA men, GPRC5C R14Q was 0.76% and 0.08% in cases and controls, respectively, OR for PCa was 9.00 (95%CI 0.56-145.23), pexact = 0.19. However, IGF1R R511Q was not found in cases or controls. CONCLUSIONS This WES study identified two rare, recurrent nonsynonymous PCa risk-associated variants in AA. Confirmation in additional large populations of AA PCa cases and controls is required.
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Affiliation(s)
- Jun Wei
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jennifer Beebe-Dimmer
- Barabara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Christopher Sample
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Guifang Yan
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Azita Sadeghpour
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Marta Gielzak
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sodam Choi
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Moon
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
- Department of Surgery, University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Patrick C Walsh
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Kathleen A Cooney
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - William B Isaacs
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
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Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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