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Akiyama T, Raftery LA, Wharton KA. Bone morphogenetic protein signaling: the pathway and its regulation. Genetics 2024; 226:iyad200. [PMID: 38124338 PMCID: PMC10847725 DOI: 10.1093/genetics/iyad200] [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: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023] Open
Abstract
In the mid-1960s, bone morphogenetic proteins (BMPs) were first identified in the extracts of bone to have the remarkable ability to induce heterotopic bone. When the Drosophila gene decapentaplegic (dpp) was first identified to share sequence similarity with mammalian BMP2/BMP4 in the late-1980s, it became clear that secreted BMP ligands can mediate processes other than bone formation. Following this discovery, collaborative efforts between Drosophila geneticists and mammalian biochemists made use of the strengths of their respective model systems to identify BMP signaling components and delineate the pathway. The ability to conduct genetic modifier screens in Drosophila with relative ease was critical in identifying the intracellular signal transducers for BMP signaling and the related transforming growth factor-beta/activin signaling pathway. Such screens also revealed a host of genes that encode other core signaling components and regulators of the pathway. In this review, we provide a historical account of this exciting time of gene discovery and discuss how the field has advanced over the past 30 years. We have learned that while the core BMP pathway is quite simple, composed of 3 components (ligand, receptor, and signal transducer), behind the versatility of this pathway lies multiple layers of regulation that ensures precise tissue-specific signaling output. We provide a sampling of these discoveries and highlight many questions that remain to be answered to fully understand the complexity of BMP signaling.
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Affiliation(s)
- Takuya Akiyama
- Department of Biology, Rich and Robin Porter Cancer Research Center, The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA
| | - Laurel A Raftery
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
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2
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Vicidomini R, Serpe M. Local BMP signaling: A sensor for synaptic activity that balances synapse growth and function. Curr Top Dev Biol 2022; 150:211-254. [PMID: 35817503 PMCID: PMC11102767 DOI: 10.1016/bs.ctdb.2022.04.001] [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] [Indexed: 10/18/2022]
Abstract
Synapse development is coordinated by intercellular communication between the pre- and postsynaptic compartments, and by neuronal activity itself. In flies as in vertebrates, neuronal activity induces input-specific changes in the synaptic strength so that the entire circuit maintains stable function in the face of many challenges, including changes in synapse number and strength. But how do neurons sense synapse activity? In several studies carried out using the Drosophila neuromuscular junction (NMJ), we demonstrated that local BMP signaling provides an exquisite sensor for synapse activity. Here we review the main features of this exquisite sensor and discuss its functioning beyond monitoring the synapse activity but rather as a key controller that operates in coordination with other BMP signaling pathways to balance synapse growth, maturation and function.
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Affiliation(s)
- Rosario Vicidomini
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Mihaela Serpe
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States.
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3
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Zhao Q, Li Y, Du X, Chen X, Jiao Q, Jiang H. Effects of deubiquitylases on the biological behaviors of neural stem cells. Dev Neurobiol 2021; 81:847-858. [PMID: 34241974 DOI: 10.1002/dneu.22844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/16/2021] [Indexed: 11/11/2022]
Abstract
New neurons are generated throughout life in distinct regions of the mammalian brain due to the proliferation and differentiation of neural stem cells (NSCs). Ubiquitin, a post-translational modification of cellular proteins, is an important factor in regulating neurogenesis. Deubiquitination is a biochemical process that mediates the removal of ubiquitin moieties from ubiquitin-conjugated substrates. Recent studies have provided growing evidence that deubiquitylases (DUBs) which reverse ubiquitylation process play critical roles in NSCs maintenance, differentiation and maturation. This review mainly focused on the relationship of DUBs and NSCs, and further summarized recent advances in our understanding of DUBs on regulating NSCs biological behaviors.
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Affiliation(s)
- Qiqi Zhao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Yixin Li
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Xixun Du
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Xi Chen
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Qian Jiao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Hong Jiang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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4
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Nguyen TH, Han TH, Newfeld SJ, Serpe M. Selective Disruption of Synaptic BMP Signaling by a Smad Mutation Adjacent to the Highly Conserved H2 Helix. Genetics 2020; 216:159-175. [PMID: 32737119 PMCID: PMC7463279 DOI: 10.1534/genetics.120.303484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) shape normal development and function via canonical and noncanonical signaling pathways. BMPs initiate canonical signaling by binding to transmembrane receptors that phosphorylate Smad proteins and induce their translocation into the nucleus and regulation of target genes. Phosphorylated Smads also accumulate at cellular junctions, but this noncanonical, local BMP signaling modality remains less defined. We have recently reported that phosphorylated Smad (pMad in Drosophila) accumulates at synaptic junctions in protein complexes with genetically distinct composition and regulation. Here, we examined a wide collection of DrosophilaMad alleles and searched for molecular features relevant to pMad accumulation at synaptic junctions. We found that strong Mad alleles generally disrupt both synaptic and nuclear pMad, whereas moderate Mad alleles have a wider range of phenotypes and can selectively impact different BMP signaling pathways. Interestingly, regulatory Mad mutations reveal that synaptic pMad appears to be more sensitive to a net reduction in Mad levels than nuclear pMad. Importantly, a previously uncharacterized allele, Mad8 , showed markedly reduced synaptic pMad but only moderately diminished nuclear pMad. The postsynaptic composition and electrophysiological properties of Mad8 neuromuscular junctions (NMJs) were also altered. Using biochemical approaches, we examined how a single point mutation in Mad8 could influence the Mad-receptor interface and identified a key motif, the H2 helix. Our study highlights the biological relevance of Smad-dependent, synaptic BMP signaling and uncovers a highly conserved structural feature of Smads, critical for normal development and function.
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Affiliation(s)
- Tho Huu Nguyen
- Section on Cellular Communication, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Tae Hee Han
- Section on Cellular Communication, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Mihaela Serpe
- Section on Cellular Communication, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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5
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Wisotzkey RG, Newfeld SJ. TGF-β Prodomain Alignments Reveal Unexpected Cysteine Conservation Consistent with Phylogenetic Predictions of Cross-Subfamily Heterodimerization. Genetics 2020; 214:447-465. [PMID: 31843757 PMCID: PMC7017013 DOI: 10.1534/genetics.119.302255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Evolutionary relationships between prodomains in the TGF-β family have gone unanalyzed due to a perceived lack of conservation. We developed a novel approach, identified these relationships, and suggest hypotheses for new regulatory mechanisms in TGF-β signaling. First, a quantitative analysis placed each family member from flies, mice, and nematodes into the Activin, BMP, or TGF-β subfamily. Second, we defined the prodomain and ligand via the consensus cleavage site. Third, we generated alignments and trees from the prodomain, ligand, and full-length sequences independently for each subfamily. Prodomain alignments revealed that six structural features of 17 are well conserved: three in the straitjacket and three in the arm. Alignments also revealed unexpected cysteine conservation in the "LTBP-Association region" upstream of the straitjacket and in β8 of the bowtie in 14 proteins from all three subfamilies. In prodomain trees, eight clusters across all three subfamilies were present that were not seen in the ligand or full-length trees, suggesting prodomain-mediated cross-subfamily heterodimerization. Consistency between cysteine conservation and prodomain clustering provides support for heterodimerization predictions. Overall, our analysis suggests that cross-subfamily interactions are more common than currently appreciated and our predictions generate numerous testable hypotheses about TGF-β function and evolution.
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Affiliation(s)
| | - Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
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6
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Transgenic Analyses in Drosophila Reveal That mCORL1 Is Functionally Distinct from mCORL2 and dCORL. G3-GENES GENOMES GENETICS 2019; 9:3781-3789. [PMID: 31530634 PMCID: PMC6829133 DOI: 10.1534/g3.119.400647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Uncovering how new members of multigene families acquire new functions is an important topic in evolutionary and developmental genetics. CORL proteins (SKOR in mice, Fussel in humans and fussel in Flybase) are a family of CNS specific proteins related to mammalian Sno/Ski oncogenes. Drosophila CORL (dCORL) participates in TGF-β and insulin signaling during development and in adult homeostasis but roles for the two mouse CORL proteins (mCORL) are essentially unknown. A series of studies were conducted to test the hypothesis based on previous results that mCORL1 is more similar to dCORL than mCORL2. Neither an updated alignment nor ectopic expression in adult wings were able to distinguish mCORL1 or mCORL2 from dCORL. Transgene experiments employing a dCORL endogenous function in mushroom body neurons showed that mCORL1 is distinct from mCORL2 and dCORL. mCORL1 and mCORL2 are also distinct in biochemical assays of Smad-binding and BMP signaling. Taken together, the data suggests testable new hypotheses for mCORL2 function in mammalian TGF-β and insulin signaling based on known roles for dCORL. Overall, the study reiterates the value of transgenic methods in Drosophila to provide new information on multigene family evolution and the function of family members in other species.
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7
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Deubiquitinating Enzymes and Bone Remodeling. Stem Cells Int 2018; 2018:3712083. [PMID: 30123285 PMCID: PMC6079350 DOI: 10.1155/2018/3712083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/29/2018] [Indexed: 02/05/2023] Open
Abstract
Bone remodeling, which is essential for bone homeostasis, is controlled by multiple factors and mechanisms. In the past few years, studies have emphasized the role of the ubiquitin-dependent proteolysis system in regulating bone remodeling. Deubiquitinases, which are grouped into five families, remove ubiquitin from target proteins and are involved in several cell functions. Importantly, a number of deubiquitinases mediate bone remodeling through regulating differentiation and/or function of osteoblast and osteoclasts. In this review, we review the functions and mechanisms of deubiquitinases in mediating bone remodeling.
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Upadhyay A, Moss-Taylor L, Kim MJ, Ghosh AC, O'Connor MB. TGF-β Family Signaling in Drosophila. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a022152. [PMID: 28130362 DOI: 10.1101/cshperspect.a022152] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The transforming growth factor β (TGF-β) family signaling pathway is conserved and ubiquitous in animals. In Drosophila, fewer representatives of each signaling component are present compared with vertebrates, simplifying mechanistic study of the pathway. Although there are fewer family members, the TGF-β family pathway still regulates multiple and diverse functions in Drosophila. In this review, we focus our attention on several of the classic and best-studied functions for TGF-β family signaling in regulating Drosophila developmental processes such as embryonic and imaginal disc patterning, but we also describe several recently discovered roles in regulating hormonal, physiological, neuronal, innate immunity, and tissue homeostatic processes.
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Affiliation(s)
- Ambuj Upadhyay
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lindsay Moss-Taylor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Myung-Jun Kim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Arpan C Ghosh
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael B O'Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
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9
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Quijano JC, Wisotzkey RG, Tran NL, Huang Y, Stinchfield MJ, Haerry TE, Shimmi O, Newfeld SJ. lolal Is an Evolutionarily New Epigenetic Regulator of dpp Transcription during Dorsal-Ventral Axis Formation. Mol Biol Evol 2016; 33:2621-32. [PMID: 27401231 PMCID: PMC5026256 DOI: 10.1093/molbev/msw132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Secreted ligands in the Dpp/BMP family drive dorsal–ventral (D/V) axis formation in all Bilaterian species. However, maternal factors regulating Dpp/BMP transcription in this process are largely unknown. We identified the BTB domain protein longitudinals lacking-like (lolal) as a modifier of decapentaplegic (dpp) mutations. We show that Lolal is evolutionarily related to the Trithorax group of chromatin regulators and that lolal interacts genetically with the epigenetic factor Trithorax-like during Dpp D/V signaling. Maternally driven LolalHA is found in oocytes and translocates to zygotic nuclei prior to the point at which dpp transcription begins. lolal maternal and zygotic mutant embryos display significant reductions in dpp, pMad, and zerknullt expression, but they are never absent. The data suggest that lolal is required to maintain dpp transcription during D/V patterning. Phylogenetic data revealed that lolal is an evolutionarily new gene present only in insects and crustaceans. We conclude that Lolal is the first maternal protein identified with a role in dpp D/V transcriptional maintenance, that Lolal and the epigenetic protein Trithorax-like are essential for Dpp D/V signaling and that the architecture of the Dpp D/V pathway evolved in the arthropod lineage after the separation from vertebrates via the incorporation of new genes such as lolal.
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Affiliation(s)
| | | | | | - Yunxian Huang
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Theodor E Haerry
- Center for Molecular Biology and Biotechnology, Florida Atlantic University
| | - Osamu Shimmi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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10
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Liu S, de Boeck M, van Dam H, ten Dijke P. Regulation of the TGF-β pathway by deubiquitinases in cancer. Int J Biochem Cell Biol 2016; 76:135-45. [DOI: 10.1016/j.biocel.2016.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 11/26/2022]
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11
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A microRNA code for prostate cancer metastasis. Oncogene 2015; 35:1180-92. [PMID: 26073083 PMCID: PMC4803473 DOI: 10.1038/onc.2015.176] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023]
Abstract
Although the development of bone metastasis is a major detrimental event in prostate cancer, the molecular mechanisms responsible for bone homing and destruction remain largely unknown. Here we show that loss of miR-15 and miR-16 in cooperation with increased miR-21 expression promote prostate cancer spreading and bone lesions. This combination of microRNA endows bone-metastatic potential to prostate cancer cells. Concomitant loss of miR-15/miR-16 and gain of miR-21 aberrantly activate TGF-β and Hedgehog signaling, that mediate local invasion, distant bone marrow colonization and osteolysis by prostate cancer cells. These findings establish a new molecular circuitry for prostate cancer metastasis that was validated in patients' cohorts. Our data indicate a network of biomarkers and druggable pathways to improve patient treatment.
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12
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Murtaza M, Jolly LA, Gecz J, Wood SA. La FAM fatale: USP9X in development and disease. Cell Mol Life Sci 2015; 72:2075-89. [PMID: 25672900 PMCID: PMC4427618 DOI: 10.1007/s00018-015-1851-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/12/2022]
Abstract
Deubiquitylating enzymes (DUBs), act downstream of ubiquitylation. As such, these post-post-translational modifiers function as the final arbitrators of a protein substrate’s ubiquitylation status, thus regulating its fate. In most instances, DUBs moderate the absolute level of a substrate, its locality or activity, rather than being an “all-or-none” phenomenon. Yet, disruption of this quantitative regulation can produce dramatic qualitative differences. The ubiquitin-specific protease 9X (USP9X/FAM) is a substrate-specific DUB, which displays an extraordinarily high level of sequence conservation from Drosophila to mammals. It is primarily the recent revelations of USP9X’s pivotal role in human cancers, both as oncogene or tumour suppressor, in developmental disorders including intellectual disability, epilepsy, autism and developmental delay that has led to a subsequent re-examination of its molecular and cellular functions. Results from experimental animal models have implicated USP9X in neurodegeneration, including Parkinson’s and Alzheimer’s disease, as well as autoimmune diseases. In this review, we describe the current and accumulated knowledge on the molecular, cellular and developmental aspects of USP9X function within the context of the biological consequences during normal development and disease.
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Affiliation(s)
- Mariyam Murtaza
- The Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
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Herhaus L, Sapkota GP. The emerging roles of deubiquitylating enzymes (DUBs) in the TGFβ and BMP pathways. Cell Signal 2014; 26:2186-92. [PMID: 25007997 PMCID: PMC4443431 DOI: 10.1016/j.cellsig.2014.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 06/27/2014] [Indexed: 12/20/2022]
Abstract
The members of the transforming growth factor beta (TGFβ) family of cytokines, including bone morphogenetic proteins (BMP), play fundamental roles in development and tissue homeostasis. Hence, aberrant TGFβ/BMP signalling is associated with several human diseases such as fibrosis, bone and immune disorders, cancer progression and metastasis. Consequently, targeting TGFβ signalling for intervention potentially offers therapeutic opportunities against these diseases. Many investigations have focussed on understanding the molecular mechanisms underpinning the regulation of TGFβ signalling. One of the key areas has been to investigate the regulation of the protein components of the TGFβ/BMP signal transduction pathways by ubiquitylation and deubiquitylation. In the last 15years, extensive research has led to the discovery and characterisation of several E3 ubiquitin ligases that influence the TGFβ pathway. However, the research on DUBs regulating the TGFβ pathway has received prominence only recently and is still an emerging field. This review will provide a concise summary of our current understanding of how DUBs regulate TGFβ signalling.
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Affiliation(s)
- Lina Herhaus
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland, United Kingdom
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland, United Kingdom.
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Peterson AJ, O'Connor MB. Strategies for exploring TGF-β signaling in Drosophila. Methods 2014; 68:183-93. [PMID: 24680699 PMCID: PMC4057889 DOI: 10.1016/j.ymeth.2014.03.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 02/06/2023] Open
Abstract
The TGF-β pathway is an evolutionarily conserved signal transduction module that mediates diverse biological processes in animals. In Drosophila, both the BMP and Activin branches are required for viability. Studies rooted in classical and molecular genetic approaches continue to uncover new developmental roles for TGF-β signaling. We present an overview of the secreted ligands, transmembrane receptors and cellular Smad transducer proteins that compose the core pathway in Drosophila. An assortment of tools have been developed to conduct tissue-specific loss- and gain-of-function experiments for these pathway components. We discuss the deployment of these reagents, with an emphasis on appropriate usage and limitations of the available tools. Throughout, we note reagents that are in need of further improvement or development, and signaling features requiring further study. A general theme is that comparison of phenotypes for ligands, receptors, and Smads can be used to map tissue interactions, and to separate canonical and non-canonical signaling activities. Core TGF-β signaling components are subject to multiple layers of regulation, and are coupled to context-specific inputs and outputs. In addition to fleshing out how TGF-β signaling serves the fruit fly, we anticipate that future studies will uncover new regulatory nodes and modes and will continue to advance paradigms for how TGF-β signaling regulates general developmental processes.
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Affiliation(s)
- Aidan J Peterson
- Department of Genetics, Cell Biology & Development, 6-160 Jackson Hall, 321 Church St SE, University of Minnesota, Minneapolis, MN 55455, United States
| | - Michael B O'Connor
- Department of Genetics, Cell Biology & Development, 6-160 Jackson Hall, 321 Church St SE, University of Minnesota, Minneapolis, MN 55455, United States.
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15
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Wisotzkey RG, Quijano JC, Stinchfield MJ, Newfeld SJ. New gene evolution in the bonus-TIF1-γ/TRIM33 family impacted the architecture of the vertebrate dorsal-ventral patterning network. Mol Biol Evol 2014; 31:2309-21. [PMID: 24881051 DOI: 10.1093/molbev/msu175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Uncovering how a new gene acquires its function and understanding how the function of a new gene influences existing genetic networks are important topics in evolutionary biology. Here, we demonstrate nonconservation for the embryonic functions of Drosophila Bonus and its newest vertebrate relative TIF1-γ/TRIM33. We showed previously that TIF1-γ/TRIM33 functions as an ubiquitin ligase for the Smad4 signal transducer and antagonizes the Bone Morphogenetic Protein (BMP) signaling network underlying vertebrate dorsal-ventral axis formation. Here, we show that Bonus functions as an agonist of the Decapentaplegic (Dpp) signaling network underlying dorsal-ventral axis formation in flies. The absence of conservation for the roles of Bonus and TIF1-γ/TRIM33 reveals a shift in the dorsal-ventral patterning networks of flies and mice, systems that were previously considered wholly conserved. The shift occurred when the new gene TIF1-γ/TRIM33 replaced the function of the ubiquitin ligase Nedd4L in the lineage leading to vertebrates. Evidence of this replacement is our demonstration that Nedd4 performs the function of TIF1-γ/TRIM33 in flies during dorsal-ventral axis formation. The replacement allowed vertebrate Nedd4L to acquire novel functions as a ubiquitin ligase of vertebrate-specific Smad proteins. Overall our data reveal that the architecture of the Dpp/BMP dorsal-ventral patterning network continued to evolve in the vertebrate lineage, after separation from flies, via the incorporation of new genes.
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Affiliation(s)
- Robert G Wisotzkey
- Department of Biological Sciences, California State University, East Bay
| | - Janine C Quijano
- Department of Biological Sciences, California State University, East BaySchool of Life Sciences, Arizona State University
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16
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Homan CC, Kumar R, Nguyen LS, Haan E, Raymond FL, Abidi F, Raynaud M, Schwartz CE, Wood SA, Gecz J, Jolly LA. Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth. Am J Hum Genet 2014; 94:470-8. [PMID: 24607389 DOI: 10.1016/j.ajhg.2014.02.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/13/2014] [Indexed: 11/17/2022] Open
Abstract
With a wealth of disease-associated DNA variants being recently reported, the challenges of providing their functional characterization are mounting. Previously, as part of a large systematic resequencing of the X chromosome in 208 unrelated families with nonsyndromic X-linked intellectual disability, we identified three unique variants (two missense and one protein truncating) in USP9X. To assess the functional significance of these variants, we took advantage of the Usp9x knockout mouse we generated. Loss of Usp9x causes reduction in both axonal growth and neuronal cell migration. Although overexpression of wild-type human USP9X rescued these defects, all three USP9X variants failed to rescue axonal growth, caused reduced USP9X protein localization in axonal growth cones, and (in 2/3 variants) failed to rescue neuronal cell migration. Interestingly, in one of these families, the proband was subsequently identified to have a microdeletion encompassing ARID1B, a known ID gene. Given our findings it is plausible that loss of function of both genes contributes to the individual's phenotype. This case highlights the complexity of the interpretations of genetic findings from genome-wide investigations. We also performed proteomics analysis of neurons from both the wild-type and Usp9x knockout embryos and identified disruption of the cytoskeleton as the main underlying consequence of the loss of Usp9x. Detailed clinical assessment of all three families with USP9X variants identified hypotonia and behavioral and morphological defects as common features in addition to ID. Together our data support involvement of all three USP9X variants in ID in these families and provide likely cellular and molecular mechanisms involved.
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Affiliation(s)
- Claire C Homan
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Raman Kumar
- Women's and Children's Health Research Institute, North Adelaide, SA 5006, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia; School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lam Son Nguyen
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia
| | - Eric Haan
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Clinical Genetics Service, SA Pathology at Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Fatima Abidi
- J.C. Self Research Institute, Greenwood Genetics Centre, Greenwood, SC 29646, USA
| | - Martine Raynaud
- CHRU de Tours, Service de Génétique, Tours 37000, France; Inserm U930, UMR Imagerie et Cerveau, Tours 37000, France
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetics Centre, Greenwood, SC 29646, USA
| | - Stephen A Wood
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Jozef Gecz
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia; Women's and Children's Health Research Institute, North Adelaide, SA 5006, Australia; School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Lachlan A Jolly
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Institute, University of Adelaide, Adelaide, SA 5005, Australia.
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17
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Loss of Usp9x disrupts cortical architecture, hippocampal development and TGFβ-mediated axonogenesis. PLoS One 2013; 8:e68287. [PMID: 23861879 PMCID: PMC3702552 DOI: 10.1371/journal.pone.0068287] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/28/2013] [Indexed: 01/17/2023] Open
Abstract
The deubiquitylating enzyme Usp9x is highly expressed in the developing mouse brain, and increased Usp9x expression enhances the self-renewal of neural progenitors in vitro. USP9X is a candidate gene for human neurodevelopmental disorders, including lissencephaly, epilepsy and X-linked intellectual disability. To determine if Usp9x is critical to mammalian brain development we conditionally deleted the gene from neural progenitors, and their subsequent progeny. Mating Usp9xloxP/loxP mice with mice expressing Cre recombinase from the Nestin promoter deleted Usp9x throughout the entire brain, and resulted in early postnatal lethality. Although the overall brain architecture was intact, loss of Usp9x disrupted the cellular organization of the ventricular and sub-ventricular zones, and cortical plate. Usp9x absence also led to dramatic reductions in axonal length, in vivo and in vitro, which could in part be explained by a failure in Tgf-β signaling. Deletion of Usp9x from the dorsal telencephalon only, by mating with Emx1-cre mice, was compatible with survival to adulthood but resulted in reduction or loss of the corpus callosum, a dramatic decrease in hippocampal size, and disorganization of the hippocampal CA3 region. This latter phenotypic aspect resembled that observed in Doublecortin knock-out mice, which is an Usp9x interacting protein. This study establishes that Usp9x is critical for several aspects of CNS development, and suggests that its regulation of Tgf-β signaling extends to neurons.
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18
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Shimmi O, Newfeld SJ. New insights into extracellular and post-translational regulation of TGF-β family signalling pathways. J Biochem 2013; 154:11-9. [PMID: 23698094 PMCID: PMC3693483 DOI: 10.1093/jb/mvt046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 05/08/2013] [Indexed: 01/19/2023] Open
Abstract
Members of the transforming growth factor-β (TGF-β) family of secreted proteins are present in all multicellular animals. TGF-β proteins are versatile intercellular signalling molecules that orchestrate cell fate decisions during development and maintain homeostasis in adults. The Smad family of signal transducers implements TGF-β signals in responsive cells. Given the ability of TGF-β ligands to induce dramatic responses in target cells, numerous regulatory mechanisms exist to prevent unintended consequences. Here we review new reports of extracellular and post-translational regulation in Drosophila and vertebrates. Extracellular topics include the regulation of TGF-β signalling range and the coordination between tissue morphogenesis and TGF-β signalling. Post-translational topics include the regulation of TGF-β signal transduction by Gsk3-β phosphorylation of Smads and by cycles of Smad mono- and deubiquitylation. Extension of the ubiquitylation data to the Hippo pathway is also discussed.
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Affiliation(s)
- Osamu Shimmi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland and School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Stuart J. Newfeld
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland and School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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19
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Wisotzkey RG, Konikoff CE, Newfeld SJ. Hippo pathway phylogenetics predicts monoubiquitylation of Salvador and Merlin/Nf2. PLoS One 2012; 7:e51599. [PMID: 23272121 PMCID: PMC3522738 DOI: 10.1371/journal.pone.0051599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 11/08/2012] [Indexed: 01/20/2023] Open
Abstract
Recently we employed phylogenetics to predict that the cellular interpretation of TGF-β signals is modulated by monoubiquitylation cycles affecting the Smad4 signal transducer/tumor suppressor. This prediction was subsequently validated by experiments in flies, frogs and mammalian cells. Here we apply a phylogenetic approach to the Hippo pathway and predict that two of its signal transducers, Salvador and Merlin/Nf2 (also a tumor suppressor) are regulated by monoubiquitylation. This regulatory mechanism does not lead to protein degradation but instead serves as a highly efficient “off/on” switch when the protein is subsequently deubiquitylated. Overall, our study shows that the creative application of phylogenetics can predict new roles for pathway components and new mechanisms for regulating intercellular signaling pathways.
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Affiliation(s)
| | - Charlotte E. Konikoff
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Stuart J. Newfeld
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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20
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Dupont S, Inui M, Newfeld SJ. Regulation of TGF-β signal transduction by mono- and deubiquitylation of Smads. FEBS Lett 2012; 586:1913-20. [PMID: 22710170 PMCID: PMC3383349 DOI: 10.1016/j.febslet.2012.03.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/17/2012] [Accepted: 03/19/2012] [Indexed: 01/17/2023]
Abstract
Polyubiquitylation leading to proteasomal degradation is a well-established mechanism for regulating TGF-β signal transduction components such as receptors and Smads. Recently, an equally important role was suggested for monoubiquitylation of both Smad4 and receptor-associated Smads that regulates their function without protein degradation. Monoubiquitylation of Smads was discovered following the identification of deubiquitylases required for TGF-β signaling, suggesting that continuous cycles of Smad mono- and deubiquitylation are required for proper TGF-β signal transduction. Here we summarize and discuss recent work on Smad mono- and deubiquitylation.
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Affiliation(s)
- Sirio Dupont
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Masafumi Inui
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Stuart J. Newfeld
- School of Life Sciences, Arizona State University, Tempe AZ 85287-4501, USA
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