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1.
Bioessays ; : e2400127, 2024 Aug 28.
Article in English | MEDLINE | ID: mdl-39194376

ABSTRACT

Cells utilize diverse organelles to maintain homeostasis and to respond to extracellular stimuli. Recently, multifaceted aspects of organelle stress caused by various factors have been emerging. The endosome is an essential organelle, functioning as the central hub for membrane trafficking in cooperation with the ubiquitin system. However, knowledge regarding endosomal stress, which refers to organelle stress of the endosome, is currently limited. We recently revealed ubiquitin-mediated endosomal stress of early endosomes (EEs) and its responsive signaling pathways. These findings shed light on the relevance of ubiquitin-mediated endosomal stress to physiological and pathological processes. Here, we present a hypothesis that ubiquitin-mediated endosomal stress may have significant roles in biological contexts and that ubiquitin-specific protease 8 is a key regulator of ubiquitin clearance from EEs.

2.
Mol Biol Evol ; 39(2)2022 02 03.
Article in English | MEDLINE | ID: mdl-34999820

ABSTRACT

The molecular evolution processes underlying the acquisition of the placenta in eutherian ancestors are not fully understood. Mouse NCK-interacting kinase (NIK)-related kinase (NRK) is expressed highly in the placenta and plays a role in preventing placental hyperplasia. Here, we show the molecular evolution of NRK, which confers its function for inhibiting placental cell proliferation. Comparative genome analysis identified NRK orthologs across vertebrates, which share the kinase and citron homology (CNH) domains. Evolutionary analysis revealed that NRK underwent extensive amino acid substitutions in the ancestor of placental mammals and has been since conserved. Biochemical analysis of mouse NRK revealed that the CNH domain binds to phospholipids, and a region in NRK binds to and inhibits casein kinase-2 (CK2), which we named the CK2-inhibitory region (CIR). Cell culture experiments suggest the following: 1) Mouse NRK is localized at the plasma membrane via the CNH domain, where the CIR inhibits CK2. 2) This mitigates CK2-dependent phosphorylation and inhibition of PTEN and 3) leads to the inhibition of AKT signaling and cell proliferation. Nrk deficiency increased phosphorylation levels of PTEN and AKT in mouse placenta, supporting our hypothesis. Unlike mouse NRK, chicken NRK did not bind to phospholipids and CK2, decrease phosphorylation of AKT, or inhibit cell proliferation. Both the CNH domain and CIR have evolved under purifying selection in placental mammals. Taken together, our study suggests that placental mammals acquired the phospholipid-binding CNH domain and CIR in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation.


Subject(s)
Casein Kinase II , Intracellular Signaling Peptides and Proteins/genetics , PTEN Phosphohydrolase , Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins c-akt , Animals , Casein Kinase II/genetics , Casein Kinase II/metabolism , Cell Proliferation , Eutheria/metabolism , Female , Mice , PTEN Phosphohydrolase/genetics , PTEN Phosphohydrolase/metabolism , Phosphorylation , Placenta/metabolism , Pregnancy , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism
3.
J Reprod Dev ; 69(1): 32-40, 2023 Feb 08.
Article in English | MEDLINE | ID: mdl-36567126

ABSTRACT

In mice and humans, Nik-related protein kinase (Nrk) is an X-linked gene that encodes a serine/threonine kinase belonging to GCK group 4. Nrk knockout (Nrk KO) mice exhibit delayed delivery, possibly due to defective communication between the Nrk KO conceptus and its mother. However, the mechanism of delayed labor remains largely unknown. Here, we found that in pregnant mothers with the Nrk KO conceptus, the serum progesterone (P4) and placental lactogen (PL-2) concentrations in late pregnancy were higher than those in the wild type. Moreover, we demonstrated that Nrk is expressed in trophoblast giant cells (TGCs) and syncytiotrophoblast-2 (SynT-2) in the labyrinth layer of the mouse placenta. In the human placenta, NRK is also expressed in Syn-T in villi. Both human Syn-T and mouse TGCs of the labyrinth layer are present within fetal tissues that are in direct contact with the maternal blood. The labyrinth layer of the Nrk KO conceptus was gigantic, with enlarged cytoplasm and Golgi bodies in the TGCs. To investigate the function of Nrk in the labyrinth layer, a differentially expressed gene (DEG) analysis was performed. The DEG analysis revealed that labor-promoting factors, such as prostaglandins, were decreased, and pregnancy-maintaining factors, such as the prolactin family and P4 receptor, were increased. These findings suggest that the Nrk KO mice exhibit delayed delivery owing to high P4 concentrations caused by the hypersecretion of pregnancy-maintaining factors, such as PL-2, from the placenta.


Subject(s)
Placenta , Protein Serine-Threonine Kinases , Humans , Pregnancy , Mice , Female , Animals , Placenta/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Trophoblasts/metabolism , Mice, Knockout , Prolactin/metabolism
4.
J Cell Sci ; 132(3)2019 02 07.
Article in English | MEDLINE | ID: mdl-30659120

ABSTRACT

Endocytic trafficking is regulated by ubiquitylation (also known as ubiquitination) of cargoes and endocytic machineries. The role of ubiquitylation in lysosomal delivery has been well documented, but its role in the recycling pathway is largely unknown. Here, we report that the ubiquitin (Ub) ligase RFFL regulates ubiquitylation of endocytic recycling regulators. An RFFL dominant-negative (DN) mutant induced clustering of endocytic recycling compartments (ERCs) and delayed endocytic cargo recycling without affecting lysosomal traffic. A BioID RFFL interactome analysis revealed that RFFL interacts with the Rab11 effectors EHD1, MICALL1 and class I Rab11-FIPs. The RFFL DN mutant strongly captured these Rab11 effectors and inhibited their ubiquitylation. The prolonged interaction of RFFL with Rab11 effectors was sufficient to induce the clustered ERC phenotype and to delay cargo recycling. RFFL directly ubiquitylates these Rab11 effectors in vitro, but RFFL knockout (KO) only reduced the ubiquitylation of Rab11-FIP1. RFFL KO had a minimal effect on the ubiquitylation of EHD1, MICALL1, and Rab11-FIP2, and failed to delay transferrin recycling. These results suggest that multiple Ub ligases including RFFL regulate the ubiquitylation of Rab11 effectors, determining the integral function of the ERC.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Endosomes/metabolism , Membrane Proteins/metabolism , Microfilament Proteins/metabolism , Protein Processing, Post-Translational , Vesicular Transport Proteins/metabolism , rab GTP-Binding Proteins/metabolism , Adaptor Proteins, Signal Transducing/genetics , Biological Transport , Cell Line , Endocytosis/genetics , HEK293 Cells , HeLa Cells , Humans , Lysosomes/metabolism , Membrane Proteins/genetics , Microfilament Proteins/genetics , Protein Binding , Protein Interaction Mapping , Transferrin/genetics , Transferrin/metabolism , Ubiquitination , Vesicular Transport Proteins/genetics , rab GTP-Binding Proteins/genetics
5.
J Biol Chem ; 294(44): 16429-16439, 2019 11 01.
Article in English | MEDLINE | ID: mdl-31533987

ABSTRACT

Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain-containing protein 8 (SET8) is the sole enzyme that monomethylates Lys-20 of histone H4 (H4K20). SET8 has been implicated in the regulation of multiple biological processes, such as gene transcription, the cell cycle, and senescence. SET8 quickly undergoes ubiquitination and degradation by several E3 ubiquitin ligases; however, the enzyme that deubiquitinates SET8 has not yet been identified. Here we demonstrated that ubiquitin-specific peptidase 17-like family member (USP17) deubiquitinates and therefore stabilizes the SET8 protein. We observed that USP17 interacts with SET8 and removes polyubiquitin chains from SET8. USP17 knockdown not only decreased SET8 protein levels and H4K20 monomethylation but also increased the levels of the cyclin-dependent kinase inhibitor p21. As a consequence, USP17 knockdown suppressed cell proliferation. We noted that USP17 was down-regulated in replicative senescence and that USP17 inhibition alone was sufficient to trigger cellular senescence. These results reveal a regulatory mechanism whereby USP17 prevents cellular senescence by removing ubiquitin marks from and stabilizing SET8 and transcriptionally repressing p21.


Subject(s)
Cyclin-Dependent Kinase Inhibitor p21/metabolism , Endopeptidases/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Aging/metabolism , Animals , COS Cells , Cell Cycle/physiology , Cell Line , Cell Proliferation/physiology , Chlorocebus aethiops , HCT116 Cells , Histones/metabolism , Humans , MCF-7 Cells , Methyltransferases/metabolism , Protein Processing, Post-Translational , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination/physiology
6.
J Cell Sci ; 131(8)2018 04 12.
Article in English | MEDLINE | ID: mdl-29567855

ABSTRACT

Stress granules are transient cytoplasmic foci induced by various stresses that contain translation-stalled mRNAs and RNA-binding proteins. They are proposed to modulate mRNA translation and stress responses. Here, we show that the deubiquitylases USP5 and USP13 are recruited to heat-induced stress granules. Heat-induced stress granules also contained K48- and K63-linked ubiquitin chains. Depletion of USP5 or USP13 resulted in elevated ubiquitin chain levels and accelerated assembly of heat-induced stress granules, suggesting that these enzymes regulate the stability of the stress granules through their ubiquitin isopeptidase activity. Moreover, disassembly of heat-induced stress granules after returning the cells to normal temperatures was markedly repressed by individual depletion of USP5 or USP13. Finally, overexpression of a ubiquitin mutant lacking the C-terminal diglycine motif caused the accumulation of unanchored ubiquitin chains and the repression of the disassembly of heat-induced stress granules. As unanchored ubiquitin chains are preferred substrates for USP5, we suggest that USP5 regulates the assembly and disassembly of heat-induced stress granules by mediating the hydrolysis of unanchored ubiquitin chains while USP13 regulates stress granules through deubiquitylating protein-conjugated ubiquitin chains.This article has an associated First Person interview with the first author of the paper.


Subject(s)
Endopeptidases/metabolism , Humans , Hydrolysis , Protein Binding , Ubiquitin-Specific Proteases , Ubiquitination
7.
J Neurosci ; 38(28): 6267-6282, 2018 07 11.
Article in English | MEDLINE | ID: mdl-29907663

ABSTRACT

Disorganization of nodes of Ranvier is associated with motor and sensory dysfunctions. Mechanisms that allow nodal recovery during pathological processes remain poorly understood. A highly enriched nodal cytoskeletal protein ßIV spectrin anchors and stabilizes the nodal complex to actin cytoskeleton. Loss of murine ßIV spectrin allows the initial nodal organization, but causes gradual nodal destabilization. Mutations in human ßIV spectrin cause auditory neuropathy and impairment in motor coordination. Similar phenotypes are caused by nodal disruption due to demyelination. Here we report on the precise timelines of nodal disorganization and reorganization by following disassembly and reassembly of key nodal proteins in ßIV spectrin mice of both sexes before and after ßIV spectrin re-expression at specifically chosen developmental time points. We show that the timeline of nodal restoration has different outcomes in the PNS and CNS with respect to nodal reassembly and functional restoration. In the PNS, restoration of nodes occurs within 1 month regardless of the time of ßIV spectrin re-expression. In contrast, the CNS nodal reorganization and functional restoration occurs within a critical time window; after that, nodal reorganization diminishes, leading to less efficient motor recovery. We demonstrate that timely restoration of nodes can improve both the functional properties and the ultrastructure of myelinated fibers affected by long-term nodal disorganization. Our studies, which indicate a critical timeline for nodal restoration together with overall motor performance and prolonged life span, further support the idea that nodal restoration is more beneficial if initiated before any axonal damage, which is critically relevant to demyelinating disorders.SIGNIFICANCE STATEMENT Nodes of Ranvier are integral to efficient and rapid signal transmission along myelinated fibers. Various demyelinating disorders are characterized by destabilization of the nodal molecular complex, accompanied by severe reduction in nerve conduction and the onset of motor and sensory dysfunctions. This study is the first to report in vivo reassembly of destabilized nodes with sequential improvement in overall motor performance. Our study reveals that nodal restoration is achievable before any axonal damage, and that long-term nodal destabilization causes irreversible axonal structural changes that prevent functional restoration. Our studies provide significant insights into timely restoration of nodal domains as a potential therapeutic approach in treatment of demyelinating disorders.


Subject(s)
Nerve Degeneration/metabolism , Nerve Degeneration/pathology , Psychomotor Performance/physiology , Ranvier's Nodes/metabolism , Ranvier's Nodes/pathology , Animals , Mice , Mice, Mutant Strains , Mutation , Nerve Tissue Proteins/genetics , Paresis/genetics , Paresis/metabolism , Paresis/pathology , Ranvier's Nodes/ultrastructure , Recovery of Function/physiology , Sciatic Nerve/metabolism , Sciatic Nerve/pathology , Sciatic Nerve/ultrastructure , Spectrin/genetics , Spinal Cord/metabolism , Spinal Cord/pathology , Spinal Cord/ultrastructure
8.
Biochem Biophys Res Commun ; 499(3): 635-641, 2018 05 15.
Article in English | MEDLINE | ID: mdl-29604273

ABSTRACT

Nascent cargo proteins in the endoplasmic reticulum are transported to the Golgi by COPII carriers. Typical COPII vesicles are 60-70 nm in diameter, and much larger macromolecules, such as procollagen, are transported by atypical large COPII carriers in mammalian cells. The formation of large COPII carriers is enhanced by Cul3 ubiquitin ligase, which mono-ubiquitinates Sec31A, a COPII coat protein. However, the deubiquitinating enzyme for Sec31A was unclear. Here, we show that the deubiquitinating enzyme USP8 interacts with and deubiquitinates Sec31A. The interaction was mediated by the adaptor protein STAM1. USP8 overexpression inhibited the formation of large COPII carriers. By contrast, USP8 knockdown caused the accumulation of COPII coat proteins around the cis-Golgi, promoted the intracellular trafficking of procollagen IV from the endoplasmic reticulum to the Golgi, and increased collagen IV secretion. We concluded that USP8 deubiquitinates Sec31A and inhibits the formation of large COPII carriers, thereby suppressing collagen IV secretion.


Subject(s)
COP-Coated Vesicles/metabolism , Collagen Type IV/metabolism , Endopeptidases/metabolism , Endosomal Sorting Complexes Required for Transport/metabolism , Ubiquitin Thiolesterase/metabolism , Ubiquitination , Vesicular Transport Proteins/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Animals , Cell Line , Humans , Intracellular Space/metabolism , Phosphoproteins/metabolism , Protein Binding
9.
Proc Natl Acad Sci U S A ; 112(12): 3734-9, 2015 Mar 24.
Article in English | MEDLINE | ID: mdl-25775507

ABSTRACT

c-Myc protein stability and activity are tightly regulated by the ubiquitin-proteasome system. Aberrant stabilization of c-Myc contributes to many human cancers. c-Myc is ubiquitinated by SCF(Fbw7) (a SKP1-cullin-1-F-box complex that contains the F-box and WD repeat domain-containing 7, Fbw7, as the F-box protein) and several other ubiquitin ligases, whereas it is deubiquitinated and stabilized by ubiquitin-specific protease (USP) 28. The bulk of c-Myc degradation appears to occur in the nucleolus. However, whether c-Myc is regulated by deubiquitination in the nucleolus is not known. Here, we report that the nucleolar deubiquitinating enzyme USP36 is a novel c-Myc deubiquitinase. USP36 interacts with and deubiquitinates c-Myc in cells and in vitro, leading to the stabilization of c-Myc. This USP36 regulation of c-Myc occurs in the nucleolus. Interestingly, USP36 interacts with the nucleolar Fbw7γ but not the nucleoplasmic Fbw7α. However, it abolished c-Myc degradation mediated both by Fbw7γ and by Fbw7α. Consistently, knockdown of USP36 reduces the levels of c-Myc and suppresses cell proliferation. We further show that USP36 itself is a c-Myc target gene, suggesting that USP36 and c-Myc form a positive feedback regulatory loop. High expression levels of USP36 are found in a subset of human breast and lung cancers. Altogether, these results identified USP36 as a crucial and bono fide deubiquitinating enzyme controlling c-Myc's nucleolar degradation pathway.


Subject(s)
Gene Expression Regulation, Neoplastic , Neoplasms/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Ubiquitin Thiolesterase/metabolism , Breast Neoplasms/metabolism , Catalysis , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Cell Nucleolus/metabolism , Cell Nucleus/metabolism , Cell Proliferation , F-Box Proteins/metabolism , F-Box-WD Repeat-Containing Protein 7 , Female , Green Fluorescent Proteins/metabolism , HeLa Cells , Humans , Lung Neoplasms/metabolism , Microscopy, Fluorescence , Ubiquitin-Protein Ligases/metabolism
10.
J Biol Chem ; 291(12): 6218-31, 2016 Mar 18.
Article in English | MEDLINE | ID: mdl-26797118

ABSTRACT

Caveolin 1 (Cav-1) is an oligomeric protein that forms flask-shaped, lipid-rich pits, termed caveolae, on the plasma membrane. Cav-1 is targeted for lysosomal degradation in ubiquitination- and valosin-containing protein (VCP)-dependent manners. VCP, an ATPase associated with diverse cellular activities that remodels or segregates ubiquitinated protein complexes, has been proposed to disassemble Cav-1 oligomers on the endosomal membrane, facilitating the trafficking of Cav-1 to the lysosome. Genetic mutations in VCP compromise the lysosomal trafficking of Cav-1, leading to a disease called inclusion body myopathy with Paget disease of bone and/or frontotemporal dementia (IBMPFD). Here we identified the Ankrd13 family of ubiquitin-interacting motif (UIM)-containing proteins as novel VCP-interacting molecules on the endosome. Ankrd13 proteins formed a ternary complex with VCP and Cav-1 and exhibited high binding affinity for ubiquitinated Cav-1 oligomers in an UIM-dependent manner. Mass spectrometric analyses revealed that Cav-1 undergoes Lys-63-linked polyubiquitination, which serves as a lysosomal trafficking signal, and that the UIMs of Ankrd13 proteins bind preferentially to this ubiquitin chain type. The overexpression of Ankrd13 caused enlarged hollow late endosomes, which was reminiscent of the phenotype of the VCP mutations in IBMPFD. Overexpression of Ankrd13 proteins also stabilized ubiquitinated Cav-1 oligomers on the limiting membrane of enlarged endosomes. The interaction with Ankrd13 was abrogated in IMBPFD-associated VCP mutants. Collectively, our results suggest that Ankrd13 proteins cooperate with VCP to regulate the lysosomal trafficking of ubiquitinated Cav-1.


Subject(s)
Adenosine Triphosphatases/physiology , Caveolin 1/metabolism , Cell Cycle Proteins/physiology , Lysosomes/metabolism , Membrane Proteins/physiology , Animals , COS Cells , Chlorocebus aethiops , Endosomes/metabolism , HeLa Cells , Humans , Protein Binding , Protein Stability , Protein Transport , Ubiquitin/metabolism , Ubiquitinated Proteins/metabolism , Ubiquitination , Valosin Containing Protein
11.
Biochem Biophys Res Commun ; 484(3): 522-528, 2017 03 11.
Article in English | MEDLINE | ID: mdl-28126338

ABSTRACT

Insulin receptor substrates (IRSs) are phosphorylated by IGF-I receptor tyrosine kinase in a ligand-dependent manner. In turn, they bind to and activate effector proteins such as PI3K, leading to various cell responses including cell proliferation. We had reported that ubiquitin ligase Nedd4 induces mono-ubiquitination of IRS-2, thereby enhancing IRS-2 tyrosine phosphorylation, leading to increased IGF signaling and mitogenic activity. Here we show that ubiquitin-specific protease 15 (USP15) antagonizes the effect of Nedd4 on IRS-2. We identified USP15 as a protein that preferentially bound to IRS-2 when IRS-2 was conjugated with ubiquitin. In HEK293 cells, Nedd4 overexpression induced IRS-2 ubiquitination, which was decreased by USP15 co-expression while increased by USP15 knockdown. Nedd4 overexpression enhanced IGF-I-dependent IRS-2 tyrosine phosphorylation, and USP15 co-expression suppressed it. Conversely, USP15 knockdown increased IRS-2 tyrosine phosphorylation and downstream signaling in prostate cancer PC-3 cells. We concluded that USP15 attenuates IGF-I signaling by antagonizing Nedd4-induced IRS-2 ubiquitination.


Subject(s)
Endosomal Sorting Complexes Required for Transport/metabolism , Insulin Receptor Substrate Proteins/metabolism , Insulin-Like Growth Factor I/metabolism , Signal Transduction/physiology , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Specific Proteases/metabolism , Ubiquitination/physiology , HEK293 Cells , Humans , Nedd4 Ubiquitin Protein Ligases , Ubiquitinated Proteins/metabolism
12.
Am J Pathol ; 186(10): 2751-60, 2016 10.
Article in English | MEDLINE | ID: mdl-27634343

ABSTRACT

The onset and/or growth of breast tumor are controlled, at least in part, by estrogen. Therefore, to prevent the development of breast tumor, estrogen-dependent proliferation of mammary epithelial cells during pregnancy needs to be suppressed once the mammary gland is fully developed to enable lactation. However, the underlying molecular mechanisms remain unknown. Nrk is an X-linked protein serine/threonine kinase in the germinal center kinase family. Herein, we demonstrate a frequent occurrence of breast tumors in homozygous and heterozygous Nrk mutant mice that have experienced pregnancy/parturition. The tumors never developed in the mutant mice without a history of pregnancy/parturition. They exhibited histopathological features of noninvasive tubular adenocarcinoma, and expressed estrogen receptor α. At late gestation when estrogen receptor α expression was significantly reduced in the wild-type mammary gland, grossly normal mammary glands in the pregnant Nrk mutant mice occasionally contained hyperplastic foci continuously expressing the receptor. Consistently, Nrk expression was induced in the wild-type mammary gland at this period of pregnancy. On the other hand, the pregnant Nrk mutant mice also showed elevated blood estrogen levels at late gestation. We suggest that Nrk suppresses the excessive proliferation of mammary epithelial cells during pregnancy, and the impairment of this regulatory system leads to frequent occurrence of breast tumor in Nrk mutant mice.


Subject(s)
Breast Neoplasms/enzymology , Intracellular Signaling Peptides and Proteins/genetics , Mammary Neoplasms, Experimental/enzymology , Protein Serine-Threonine Kinases/genetics , Animals , Breast/metabolism , Breast/pathology , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Down-Regulation , Epithelial Cells/metabolism , Epithelial Cells/pathology , Estrogen Receptor alpha/genetics , Estrogen Receptor alpha/metabolism , Estrogens/blood , Female , Genes, X-Linked/genetics , Germinal Center Kinases , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Lactation , MCF-7 Cells , Male , Mammary Neoplasms, Experimental/genetics , Mammary Neoplasms, Experimental/pathology , Mice , Mice, Transgenic , Mutation , Pregnancy , Protein Serine-Threonine Kinases/metabolism
13.
J Biol Chem ; 289(4): 2415-23, 2014 Jan 24.
Article in English | MEDLINE | ID: mdl-24324262

ABSTRACT

Ubiquitin-specific proteases (USPs) consist of a family of deubiquitinating enzymes with more than 50 members in humans. Three of them, including USP37, contain ubiquitin-interacting motifs (UIMs), an ∼20-amino acid α-helical stretch that binds to ubiquitin. However, the roles of the UIMs in these USP enzymes remain unknown. USP37 has three UIMs, designated here as UIMs 1, 2, and 3 from the N-terminal side, between the Cys and His boxes comprising the catalytic core. Here, we examined the role of the UIMs in USP37 using its mutants that harbor mutations in the UIMs. The nuclear localization of USP37 was not affected by the UIM mutations. However, mutations in UIM2 or UIM3, but not UIM1, resulted in a significant decrease in USP37 binding to ubiquitinated proteins in the cell. In vitro, a region of USP37 harboring the three UIMs also bound to both Lys(48)-linked and Lys(63)-linked ubiquitin chains in a UIM2- and UIM3-dependent manner. The level of USP37 ubiquitination was also reduced by mutations in UIM2 or UIM3, suggesting their role in ubiquitination of USP37 itself. Finally, mutants lacking functional UIM2 or UIM3 exhibited a reduced isopeptidase activity toward ubiquitinated proteins in the cell and both Lys(48)-linked and Lys(63)-linked ubiquitin chains. These results suggested that the UIMs in USP37 contribute to the full enzymatic activity, but not ubiquitin chain substrate specificity, of USP37 possibly by holding the ubiquitin chain substrate in the proximity of the catalytic core.


Subject(s)
Endopeptidases/metabolism , Polyubiquitin/metabolism , Ubiquitinated Proteins/metabolism , Ubiquitination/physiology , Amino Acid Motifs , Animals , COS Cells , Catalysis , Chlorocebus aethiops , Endopeptidases/genetics , HeLa Cells , Humans , Mutation , Polyubiquitin/genetics , Substrate Specificity/physiology , Ubiquitinated Proteins/genetics
14.
EMBO J ; 29(13): 2114-25, 2010 Jul 07.
Article in English | MEDLINE | ID: mdl-20495530

ABSTRACT

Wingless (Wg)/Wnt has been proposed to exert various functions as a morphogen depending on the levels of its signalling. Therefore, not just the concentration of Wg/Wnt, but also the responsiveness of Wg/Wnt-target cells to the ligand, must have a crucial function in controlling cellular outputs. Here, we show that a balance of ubiquitylation and deubiquitylation of the Wg/Wnt receptor Frizzled determines the cellular responsiveness to Wg/Wnt both in mammalian cells and in Drosophila, and that the cell surface level of Frizzled is regulated by deubiquitylating enzyme UBPY/ubiquitin-specific protease 8 (USP8). Although ubiquitylated Frizzled underwent lysosomal trafficking and degradation, UBPY/USP8-dependent deubiquitylation led to recycling of Frizzled to the plasma membrane, thereby elevating its surface level. Importantly, a gain and loss of UBPY/USP8 function led to up- and down-regulation, respectively, of canonical Wg/Wnt signalling. These results unveil a novel mechanism that regulates the cellular responsiveness to Wg/Wnt by controlling the cell surface level of Frizzled.


Subject(s)
Drosophila Proteins/metabolism , Drosophila/embryology , Drosophila/metabolism , Frizzled Receptors/metabolism , Ubiquitin-Specific Proteases/metabolism , Ubiquitination , Wnt1 Protein/metabolism , Animals , Cell Line , Endocytosis , Gene Expression Regulation , Humans , Larva/metabolism , Protein Transport , Ubiquitin Thiolesterase/genetics , Ubiquitin Thiolesterase/metabolism , Wings, Animal/embryology , Wings, Animal/metabolism , Wnt Proteins/metabolism
15.
Nature ; 455(7211): 358-62, 2008 Sep 18.
Article in English | MEDLINE | ID: mdl-18758443

ABSTRACT

Deubiquitinating enzymes (DUBs) remove ubiquitin from conjugated substrates to regulate various cellular processes. The Zn(2+)-dependent DUBs AMSH and AMSH-LP regulate receptor trafficking by specifically cleaving Lys 63-linked polyubiquitin chains from internalized receptors. Here we report the crystal structures of the human AMSH-LP DUB domain alone and in complex with a Lys 63-linked di-ubiquitin at 1.2 A and 1.6 A resolutions, respectively. The AMSH-LP DUB domain consists of a Zn(2+)-coordinating catalytic core and two characteristic insertions, Ins-1 and Ins-2. The distal ubiquitin interacts with Ins-1 and the core, whereas the proximal ubiquitin interacts with Ins-2 and the core. The core and Ins-1 form a catalytic groove that accommodates the Lys 63 side chain of the proximal ubiquitin and the isopeptide-linked carboxy-terminal tail of the distal ubiquitin. This is the first reported structure of a DUB in complex with an isopeptide-linked ubiquitin chain, which reveals the mechanism for Lys 63-linkage-specific deubiquitination by AMSH family members.


Subject(s)
Lysine/metabolism , Polyubiquitin/chemistry , Polyubiquitin/metabolism , Ubiquitin Thiolesterase/chemistry , Ubiquitin Thiolesterase/metabolism , Animals , Catalysis , Conserved Sequence , Crystallography, X-Ray , Endopeptidases/chemistry , Endopeptidases/metabolism , Endosomal Sorting Complexes Required for Transport , Humans , Kinetics , Mice , Models, Molecular , Peptide Hydrolases , Polyubiquitin/genetics , Protein Structure, Tertiary , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Structure-Activity Relationship , Substrate Specificity , Ubiquitin Thiolesterase/genetics
16.
J Cell Biol ; 223(3)2024 03 04.
Article in English | MEDLINE | ID: mdl-38180476

ABSTRACT

K63-linked ubiquitin chains attached to plasma membrane proteins serve as tags for endocytosis and endosome-to-lysosome sorting. USP8 is an essential deubiquitinase for the maintenance of endosomal functions. Prolonged depletion of USP8 leads to cell death, but the major effects on cellular signaling pathways are poorly understood. Here, we show that USP8 depletion causes aberrant accumulation of K63-linked ubiquitin chains on endosomes and induces immune and stress responses. Upon USP8 depletion, two different decoders for K63-linked ubiquitin chains, TAB2/3 and p62, were recruited to endosomes and activated the TAK1-NF-κB and Keap1-Nrf2 pathways, respectively. Oxidative stress, an environmental stimulus that potentially suppresses USP8 activity, induced accumulation of K63-linked ubiquitin chains on endosomes, recruitment of TAB2, and expression of the inflammatory cytokine. The results demonstrate that USP8 is a gatekeeper of misdirected ubiquitin signals and inhibits immune and stress response pathways by removing K63-linked ubiquitin chains from endosomes.


Subject(s)
NF-E2-Related Factor 2 , NF-kappa B , Ubiquitin Thiolesterase , Endosomes/genetics , Kelch-Like ECH-Associated Protein 1/genetics , NF-E2-Related Factor 2/genetics , NF-kappa B/genetics , Ubiquitin/genetics , Humans , Ubiquitin Thiolesterase/genetics , Endosomal Sorting Complexes Required for Transport/genetics
17.
Commun Biol ; 7(1): 408, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38570609

ABSTRACT

The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.


Subject(s)
Platypus , Tachyglossidae , Animals , Phylogeny , Platypus/genetics , Tachyglossidae/genetics , Stomach , Fishes/genetics
18.
Am J Hum Genet ; 86(6): 881-91, 2010 Jun 11.
Article in English | MEDLINE | ID: mdl-20493457

ABSTRACT

A de novo 9q33.3-q34.11 microdeletion involving STXBP1 has been found in one of four individuals (group A) with early-onset West syndrome, severe hypomyelination, poor visual attention, and developmental delay. Although haploinsufficiency of STXBP1 was involved in early infantile epileptic encephalopathy in a previous different cohort study (group B), no mutations of STXBP1 were found in two of the remaining three subjects of group A (one was unavailable). We assumed that another gene within the deletion might contribute to the phenotype of group A. SPTAN1 encoding alpha-II spectrin, which is essential for proper myelination in zebrafish, turned out to be deleted. In two subjects, an in-frame 3 bp deletion and a 6 bp duplication in SPTAN1 were found at the initial nucleation site of the alpha/beta spectrin heterodimer. SPTAN1 was further screened in six unrelated individuals with WS and hypomyelination, but no mutations were found. Recombinant mutant (mut) and wild-type (WT) alpha-II spectrin could assemble heterodimers with beta-II spectrin, but alpha-II (mut)/beta-II spectrin heterodimers were thermolabile compared with the alpha-II (WT)/beta-II heterodimers. Transient expression in mouse cortical neurons revealed aggregation of alpha-II (mut)/beta-II and alpha-II (mut)/beta-III spectrin heterodimers, which was also observed in lymphoblastoid cells from two subjects with in-frame mutations. Clustering of ankyrinG and voltage-gated sodium channels at axon initial segment (AIS) was disturbed in relation to the aggregates, together with an elevated action potential threshold. These findings suggest that pathological aggregation of alpha/beta spectrin heterodimers and abnormal AIS integrity resulting from SPTAN1 mutations were involved in pathogenesis of infantile epilepsy.


Subject(s)
Developmental Disabilities/genetics , Amino Acid Sequence , Animals , Brain/metabolism , Cells, Cultured , Humans , Infant , Mice , Molecular Sequence Data , Myelin Sheath/metabolism , Phenotype , Quadriplegia/genetics , Spasms, Infantile/genetics , Spectrin/genetics , Transfection
19.
Histochem Cell Biol ; 140(2): 213-22, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23306908

ABSTRACT

Schmidt-Lanterman incisures (SLIs) are a specific feature of myelinated nerve fibers in the peripheral nervous system (PNS). In this study, we report localization of a signal transduction protein, Src, in the SLIs of mouse sciatic nerves, and its phosphorylation states in Y527 and Y418 (P527 and P418, respectively) under normal conditions or deletion of a membrane skeletal protein, 4.1G. In adult mouse sciatic nerves, Src was immunolocalized in SLIs as a cone-shape, as well as in paranodes and some areas of structures reminiscent of Cajal bands. By immunostaining in normal nerves, P527-Src was strongly detected in SLIs, whereas P418-Src was much weaker. Developmentally, P418-Src was detected in SLIs of early postnatal mouse sciatic nerves. The staining patterns for P527 and P418 in normal adult nerve fibers were opposite to those in primary culture Schwann cells and a Schwannoma cell line, RT4-D6P2T. In 4.1G-deficient nerve fibers, which had neither 4.1G nor the membrane protein palmitoylated 6 (MPP6) in SLIs, the P418-Src immunoreactivity in SLIs was clearly detected at a stronger level than that in the wild type. An immunoprecipitation study revealed Src interaction with MPP6. These findings indicate that the Src-MPP6-4.1G protein complex in SLIs has a role in signal transduction in the PNS.


Subject(s)
Guanylate Kinases/metabolism , Lipid-Linked Proteins/metabolism , Microfilament Proteins/metabolism , Nerve Fibers, Myelinated/metabolism , Peripheral Nervous System/cytology , src-Family Kinases/metabolism , Animals , Guanylate Kinases/analysis , Lipid-Linked Proteins/analysis , Membrane Proteins , Mice , Mice, Knockout , Microfilament Proteins/analysis , Microfilament Proteins/deficiency , Phosphorylation
20.
Cell Mol Life Sci ; 69(23): 4007-16, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22825661

ABSTRACT

Signal strength evoked by ligand stimulation is crucial for cellular responses such as fate decision, cell survival/death, secretion, and migration. For example, morphogens are secreted signaling molecules that form concentration gradients within tissues and induce distinct cell fates in a signal strength-dependent manner. In addition to extracellular ligand abundance, the sensitivity of signal-receiving cells to ligands also influences signal strength. Cell sensitivity to ligands is controlled at various levels: receptor presentation at the cell surface, positive/negative regulation of signal transduction, and target gene activation/repression. While the regulation of signal transduction and gene transcription is well studied, receptor presentation is still not fully understood. Recently, it was reported that cellular sensitivity to the Wingless (Wg)/Wnt morphogen is regulated by balanced ubiquitination and deubiquitination of its receptor Frizzled (Fz). In this review, we review how ubiquitination regulates receptor presentation at the cell surface for the detection of extracellular signal strength.


Subject(s)
Drosophila Proteins/metabolism , Frizzled Receptors/metabolism , Signal Transduction , Ubiquitination , Animals , Drosophila melanogaster/metabolism , Endosomes/metabolism , Lysosomes/metabolism , Models, Biological , rab GTP-Binding Proteins/metabolism
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