1
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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024; 20:1227-1236. [PMID: 38514884 DOI: 10.1038/s41589-024-01590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping.
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Affiliation(s)
- Hai-Tsang Huang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan W Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shuyao Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xu Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Yoshida Y, Takahashi T, Ishii N, Matsuo I, Takahashi S, Inoue H, Endo A, Tsuchiya H, Okada M, Ando C, Suzuki T, Dohmae N, Saeki Y, Tanaka K, Suzuki T. Sugar-mediated non-canonical ubiquitination impairs Nrf1/NFE2L1 activation. Mol Cell 2024; 84:3115-3127.e11. [PMID: 39116872 DOI: 10.1016/j.molcel.2024.07.013] [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: 10/10/2023] [Revised: 05/22/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
Proteasome is essential for cell survival, and proteasome inhibition induces proteasomal gene transcription via the activated endoplasmic-reticulum-associated transcription factor nuclear factor erythroid 2-like 1 (Nrf1/NFE2L1). Nrf1 activation requires proteolytic cleavage by DDI2 and N-glycan removal by NGLY1. We previously showed that Nrf1 ubiquitination by SKP1-CUL1-F-box (SCF)FBS2/FBXO6, an N-glycan-recognizing E3 ubiquitin ligase, impairs its activation, although the molecular mechanism remained elusive. Here, we show that SCFFBS2 cooperates with the RING-between-RING (RBR)-type E3 ligase ARIH1 to ubiquitinate Nrf1 through oxyester bonds in human cells. Endo-β-N-acetylglucosaminidase (ENGASE) generates asparagine-linked N-acetyl glucosamine (N-GlcNAc) residues from N-glycans, and N-GlcNAc residues on Nrf1 served as acceptor sites for SCFFBS2-ARIH1-mediated ubiquitination. We reconstituted the polyubiquitination of N-GlcNAc and serine/threonine residues on glycopeptides and found that the RBR-specific E2 enzyme UBE2L3 is required for the assembly of atypical ubiquitin chains on Nrf1. The atypical ubiquitin chains inhibited DDI2-mediated activation. The present results identify an unconventional ubiquitination pathway that inhibits Nrf1 activation.
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Affiliation(s)
- Yukiko Yoshida
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Satoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Haruka Inoue
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Meari Okada
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Chikara Ando
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan; Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Takeda-CiRA Joint Program (T-CiRA), 2-26-1, Muraokahigashi, Fujisawa, Kanagawa 251-8555, Japan.
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3
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van Overbeek NK, Aguirre T, van der Heden van Noort GJ, Blagoev B, Vertegaal ACO. Deciphering non-canonical ubiquitin signaling: biology and methodology. Front Mol Biosci 2024; 10:1332872. [PMID: 38414868 PMCID: PMC10897730 DOI: 10.3389/fmolb.2023.1332872] [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: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024] Open
Abstract
Ubiquitination is a dynamic post-translational modification that regulates virtually all cellular processes by modulating function, localization, interactions and turnover of thousands of substrates. Canonical ubiquitination involves the enzymatic cascade of E1, E2 and E3 enzymes that conjugate ubiquitin to lysine residues giving rise to monomeric ubiquitination and polymeric ubiquitination. Emerging research has established expansion of the ubiquitin code by non-canonical ubiquitination of N-termini and cysteine, serine and threonine residues. Generic methods for identifying ubiquitin substrates using mass spectrometry based proteomics often overlook non-canonical ubiquitinated substrates, suggesting that numerous undiscovered substrates of this modification exist. Moreover, there is a knowledge gap between in vitro studies and comprehensive understanding of the functional consequence of non-canonical ubiquitination in vivo. Here, we discuss the current knowledge about non-lysine ubiquitination, strategies to map the ubiquitinome and their applicability for studying non-canonical ubiquitination substrates and sites. Furthermore, we elucidate the available chemical biology toolbox and elaborate on missing links required to further unravel this less explored subsection of the ubiquitin system.
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Affiliation(s)
- Nila K. van Overbeek
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Tim Aguirre
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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4
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Moochickal Assainar B, Ragunathan K, Baldridge RD. Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD. Nat Commun 2024; 15:1340. [PMID: 38351109 PMCID: PMC10864399 DOI: 10.1038/s41467-024-45541-3] [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: 08/02/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
The endoplasmic reticulum associated degradation (ERAD) pathway regulates protein quality control at the endoplasmic reticulum. ERAD of lumenal and membrane proteins requires a conserved E3 ubiquitin ligase, called Hrd1. We do not understand the molecular configurations of Hrd1 that enable autoubiquitination and the subsequent retrotranslocation of misfolded protein substrates from the ER to the cytosol. Here, we have established a generalizable, single-molecule platform that enables high-efficiency labeling, stoichiometry determination, and functional assays for any integral membrane protein. Using this approach, we directly count Hrd1 proteins reconstituted into individual proteoliposomes. We report that Hrd1 assembles in different oligomeric configurations with mostly monomers and dimers detected at limiting dilution. By correlating oligomeric states with ubiquitination in vitro, we conclude that Hrd1 monomers are inefficient in autoubiquitination while dimers efficiently assemble polyubiquitin chains. Therefore, our results reveal the minimal composition of a Hrd1 oligomer that is capable of autoubiquitination. Our methods are broadly applicable to studying other complex membrane protein functions using reconstituted bilayer systems.
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Affiliation(s)
- Basila Moochickal Assainar
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Kaushik Ragunathan
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
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5
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Kamada Y, Tateishi H, Nakayamada U, Hinata D, Iwasaki A, Zhu J, Fukuda R, Okiyoneda T. UBE3C Facilitates the ER-Associated and Peripheral Degradation of Misfolded CFTR. Cells 2023; 12:2741. [PMID: 38067172 PMCID: PMC10706245 DOI: 10.3390/cells12232741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
The ubiquitin E3 ligase UBE3C promotes the proteasomal degradation of cytosolic proteins and endoplasmic reticulum (ER) membrane proteins. UBE3C is proposed to function downstream of the RNF185/MBRL ER-associated degradation (ERAD) branch, contributing to the ERAD of select membrane proteins. Here, we report that UBE3C facilitates the ERAD of misfolded CFTR, even in the absence of both RNF185 and its functional ortholog RNF5 (RNF5/185). Unlike RNF5/185, UBE3C had a limited impact on the ubiquitination of misfolded CFTR. UBE3C knockdown (KD) resulted in an additional increase in the functional ∆F508-CFTR channels on the plasma membrane when combined with the RNF5/185 ablation, particularly in the presence of clinically used CFTR modulators. Interestingly, although UBE3C KD failed to attenuate the ERAD of insig-1, it reduced the ERAD of misfolded ∆Y490-ABCB1 and increased cell surface expression. UBE3C KD also stabilized the mature form of ∆F508-CFTR and increased the cell surface level of T70-CFTR, a class VI CFTR mutant. These results suggest that UBE3C plays a vital role in the ERAD of misfolded CFTR and ABCB1, even within the RNF5/185-independent ERAD pathway, and it may also be involved in maintaining the peripheral quality control of CFTR.
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Affiliation(s)
| | | | | | | | | | | | | | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo 669-1330, Japan; (Y.K.); (H.T.); (U.N.); (D.H.); (A.I.); (J.Z.); (R.F.)
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6
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Hua Z. Deciphering the protein ubiquitylation system in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6487-6504. [PMID: 37688404 DOI: 10.1093/jxb/erad354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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7
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Dobish KK, Wittorf KJ, Swenson SA, Bean DC, Gavile CM, Woods NT, Ghosal G, Hyde RK, Buckley SM. FBXO21 mediated degradation of p85α regulates proliferation and survival of acute myeloid leukemia. Leukemia 2023; 37:2197-2208. [PMID: 37689825 PMCID: PMC10624613 DOI: 10.1038/s41375-023-02020-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by clonal expansion of myeloid blasts in the bone marrow (BM). Despite advances in therapy, the prognosis for AML patients remains poor, and there is a need to identify novel molecular pathways regulating tumor cell survival and proliferation. F-box ubiquitin E3 ligase, FBXO21, has low expression in AML, but expression correlates with survival in AML patients and patients with higher expression have poorer outcomes. Silencing FBXO21 in human-derived AML cell lines and primary patient samples leads to differentiation, inhibition of tumor progression, and sensitization to chemotherapy agents. Additionally, knockdown of FBXO21 leads to up-regulation of cytokine signaling pathways. Through a mass spectrometry-based proteomic analysis of FBXO21 in AML, we identified that FBXO21 ubiquitylates p85α, a regulatory subunit of the phosphoinositide 3-kinase (PI3K) pathway, for degradation resulting in decreased PI3K signaling, dimerization of free p85α and ERK activation. These findings reveal the ubiquitin E3 ligase, FBXO21, plays a critical role in regulating AML pathogenesis, specifically through alterations in PI3K via regulation of p85α protein stability.
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Affiliation(s)
- Kasidy K Dobish
- Department of Internal Medicine, Division of Hematology & Hematopoietic Malignancies, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Karli J Wittorf
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Samantha A Swenson
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dalton C Bean
- Department of Internal Medicine, Division of Hematology & Hematopoietic Malignancies, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, USA
| | - Catherine M Gavile
- Department of Internal Medicine, Division of Hematology & Hematopoietic Malignancies, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nicholas T Woods
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - R Katherine Hyde
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon M Buckley
- Department of Internal Medicine, Division of Hematology & Hematopoietic Malignancies, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, USA.
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8
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Liang LJ, Wang Y, Hua X, Yuan R, Xia Q, Wang R, Li C, Chu GC, Liu L, Li YM. Cell-Permeable Stimuli-Responsive Ubiquitin Probe for Time-Resolved Monitoring of Substrate Ubiquitination in Live Cells. JACS AU 2023; 3:2873-2882. [PMID: 37885572 PMCID: PMC10598832 DOI: 10.1021/jacsau.3c00421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
Dynamic monitoring of intracellular ubiquitin (Ub) conjugates is instrumental to understanding the Ub regulatory machinery. Although many biochemical approaches have been developed to characterize protein ubiquitination, chemical tools capable of temporal resolution probing of ubiquitination events remain to be developed. Here, we report the development of the first cell-permeable and stimuli-responsive Ub probe and its application for the temporal resolution profiling of ubiquitinated substrates in live cells. The probe carrying the photolabile group N-(2-nitrobenzyl)-Gly (Nbg) on the amide bond between Ub Gly75 and Gly76 is readily prepared through chemical synthesis and can be delivered to live cells by conjugation via a disulfide bond with the cyclic cell-penetrating peptide cR10D (i.e., 4-((4-(dimethylamino)phenyl)-azo)-benzoic acid-modified cyclic deca-arginine). Both in vitro and in vivo experiments showed that Ub-modifying enzymes (E1, E2s, and E3s) could not install the Ub probe onto substrate proteins prior to removal of the nitrobenzyl group, which was easily accomplished via photoirradiation. The utility and practicality of this probe were exemplified by the time-resolved biochemical and proteomic investigation of ubiquitination events in live cells during a H2O2-mediated oxidative stress response. This work shows a conceptually new family of chemical Ub tools for the time-resolved studies on dynamic protein ubiquitination in different biological processes and highlights the utility of modern chemical protein synthesis in obtaining custom-designed tools for biological studies.
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Affiliation(s)
- Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Yu Wang
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
| | - Xiao Hua
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Rujing Yuan
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
| | - Qiong Xia
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
| | - Rongtian Wang
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
| | - Chuntong Li
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Guo-Chao Chu
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
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9
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Wang X, Li Z, Shi Y, Liu Z, Zhang X, Gong Z, Yang S. Strigolactones promote plant freezing tolerance by releasing the WRKY41-mediated inhibition of CBF/DREB1 expression. EMBO J 2023; 42:e112999. [PMID: 37622245 PMCID: PMC10548171 DOI: 10.15252/embj.2022112999] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Cold stress is a major abiotic stress that adversely affects plant growth and crop productivity. The C-REPEAT BINDING FACTOR/DRE BINDING FACTOR 1 (CBF/DREB1) transcriptional regulatory cascade plays a key role in regulating cold acclimation and freezing tolerance in Arabidopsis (Arabidopsis thaliana). Here, we show that max (more axillary growth) mutants deficient in strigolactone biosynthesis and signaling display hypersensitivity to freezing stress. Exogenous application of GR245DS , a strigolactone analog, enhances freezing tolerance in wild-type plants and strigolactone-deficient mutants and promotes the cold-induced expression of CBF genes. Biochemical analysis showed that the transcription factor WRKY41 serves as a substrate for the F-box E3 ligase MAX2. WRKY41 directly binds to the W-box in the promoters of CBF genes and represses their expression, negatively regulating cold acclimation and freezing tolerance. MAX2 ubiquitinates WRKY41, thus marking it for cold-induced degradation and thereby alleviating the repression of CBF expression. In addition, SL-mediated degradation of SMXLs also contributes to enhanced plant freezing tolerance by promoting anthocyanin biosynthesis. Taken together, our study reveals the molecular mechanism underlying strigolactones promote the cold stress response in Arabidopsis.
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Affiliation(s)
- Xi Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhuoyang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiting Shi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ziyan Liu
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiaoyan Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Shuhua Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
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10
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Li Z, Li G, Li Y, Luo Y, Jiang Y, Zhang Z, Zhou Z, Liu S, Wu C, You F. Deubiquitinase OTUD6A Regulates Innate Immune Response via Targeting UBC13. Viruses 2023; 15:1761. [PMID: 37632103 PMCID: PMC10458163 DOI: 10.3390/v15081761] [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: 06/19/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
OTUD6A is a deubiquitinase that plays crucial roles in various human diseases. However, the precise regulatory mechanism of OTUD6A remains unclear. In this study, we found that OTUD6A significantly inhibited the production of type I interferon. Consistently, peritoneal macrophages and bone marrow-derived macrophages from Otud6a-/- mice produced more type I interferon after virus infection compared to cells from WT mice. Otud6a-/-- mice also exhibited increased resistance to lethal HSV-1 and VSV infections, as well as LPS attacks due to decreased inflammatory responses. Mechanistically, mass spectrometry results revealed that UBC13 was an OTUD6A-interacting protein, and the interaction was significantly enhanced after HSV-1 stimulation. Taken together, our findings suggest that OTUD6A plays a crucial role in the innate immune response and may serve as a potential therapeutic target for infectious disease.
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Affiliation(s)
- Zhiwei Li
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Guanwen Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Yunfei Li
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
| | - Yujie Luo
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
| | - Yuhan Jiang
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Ziyu Zhang
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Ziyi Zhou
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Fuping You
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
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11
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Nguyen‐Dien GT, Kozul K, Cui Y, Townsend B, Kulkarni PG, Ooi SS, Marzio A, Carrodus N, Zuryn S, Pagano M, Parton RG, Lazarou M, Millard SS, Taylor RW, Collins BM, Jones MJK, Pagan JK. FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors. EMBO J 2023; 42:e112767. [PMID: 37161784 PMCID: PMC10308361 DOI: 10.15252/embj.2022112767] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
To maintain both mitochondrial quality and quantity, cells selectively remove damaged or excessive mitochondria through mitophagy, which is a specialised form of autophagy. Mitophagy is induced in response to diverse conditions, including hypoxia, cellular differentiation and mitochondrial damage. However, the mechanisms that govern the removal of specific dysfunctional mitochondria under steady-state conditions to fine-tune mitochondrial content are not well understood. Here, we report that SCFFBXL4 , an SKP1/CUL1/F-box protein ubiquitin ligase complex, localises to the mitochondrial outer membrane in unstressed cells and mediates the constitutive ubiquitylation and degradation of the mitophagy receptors NIX and BNIP3 to suppress basal levels of mitophagy. We demonstrate that the pathogenic variants of FBXL4 that cause encephalopathic mtDNA depletion syndrome (MTDPS13) do not efficiently interact with the core SCF ubiquitin ligase machinery or mediate the degradation of NIX and BNIP3. Thus, we reveal a molecular mechanism whereby FBXL4 actively suppresses mitophagy by preventing NIX and BNIP3 accumulation. We propose that the dysregulation of NIX and BNIP3 turnover causes excessive basal mitophagy in FBXL4-associated mtDNA depletion syndrome.
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Affiliation(s)
- Giang Thanh Nguyen‐Dien
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
- Department of Biotechnology, School of BiotechnologyViet Nam National University‐International UniversityHo Chi Minh CityVietnam
| | - Keri‐Lyn Kozul
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Yi Cui
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Brendan Townsend
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | | | - Soo Siang Ooi
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Antonio Marzio
- Department of Biochemistry and Molecular PharmacologyNew York University Grossman School of MedicineNew YorkNYUSA
- Perlmutter Cancer CenterNew York University Grossman School of MedicineNew YorkNYUSA
- Department of Pathology and Lab Medicine, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Nissa Carrodus
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneQLDAustralia
| | - Michele Pagano
- Department of Biochemistry and Molecular PharmacologyNew York University Grossman School of MedicineNew YorkNYUSA
- Perlmutter Cancer CenterNew York University Grossman School of MedicineNew YorkNYUSA
| | - Robert G Parton
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
- Centre for Microscopy and MicroanalysisUniversity of QueenslandBrisbaneQLDAustralia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityMelbourneVICAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVICAustralia
| | - S Sean Millard
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
| | - Mathew JK Jones
- The University of Queensland Diamantina Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- School of Chemistry & Molecular BiosciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Julia K Pagan
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
- The University of Queensland Diamantina Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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12
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Wang W, Zhu L, Zhou J, Liu X, Xiao M, Chen N, Huang X, Chen H, Pei X, Zhang H. Targeting the KRT16-vimentin axis for metastasis in lung cancer. Pharmacol Res 2023:106818. [PMID: 37315823 DOI: 10.1016/j.phrs.2023.106818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Lung cancer is the most diagnosed malignant cancer and the leading cause of cancer-related deaths worldwide, with advanced stage and metastasis being a major issue. The mechanism leading to metastasis is not yet understood. Here, we found that KRT16 is upregulated in metastatic lung cancer tissues and correlated with poor overall survival. Knockdown of KRT16 inhibits metastasis of lung cancer both in vitro and in vivo. Mechanistically, KRT16 interacts with vimentin, and depletion of KRT16 leads to downregulation of vimentin. KRT16 acquired its oncogenic ability by stabilizing vimentin, and vimentin is required for KRT16-driven metastasis. FBXO21 mediates the polyubiquitination and degradation of KRT16, and vimentin inhibits KRT16 ubiquitination and degradation by impairing its interaction with FBXO21. Significantly, IL-15 inhibits metastasis of lung cancer in a mouse model through upregulation of FBXO21, and the level of IL-15 in circulating serum was significantly higher in nonmetastatic lung cancer patients than in metastatic patients. Our findings indicate that targeting the FBXO21/KRT16/vimentin axis may benefit lung cancer patients with metastasis.
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Affiliation(s)
- Wen Wang
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Lifei Zhu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, 510515(,) Guangzhou(,) China.
| | - Jiao Zhou
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Xiaoli Liu
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Mei Xiao
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Nan Chen
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Xiaodan Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
| | - Hongtao Chen
- Department of Laboratory, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Xiaofeng Pei
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China.
| | - Hongyu Zhang
- Department of Oncology, The fifth Affiliated Hospital of Sun Yat-sen University, 519000(,) Zhuhai(,) China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, 519000, Zhuhai, China.
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13
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Beygmoradi A, Homaei A, Hemmati R, Fernandes P. Recombinant protein expression: Challenges in production and folding related matters. Int J Biol Macromol 2023; 233:123407. [PMID: 36708896 DOI: 10.1016/j.ijbiomac.2023.123407] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Protein folding is a biophysical process by which proteins reach a specific three-dimensional structure. The amino acid sequence of a polypeptide chain contains all the information needed to determine the final three-dimensional structure of a protein. When producing a recombinant protein, several problems can occur, including proteolysis, incorrect folding, formation of inclusion bodies, or protein aggregation, whereby the protein loses its natural structure. To overcome such limitations, several strategies have been developed to address each specific issue. Identification of proper protein refolding conditions can be challenging, and to tackle this high throughput screening for different recombinant protein folding conditions can prove a sound solution. Different approaches have emerged to tackle refolding issues. One particular approach to address folding issues involves molecular chaperones, highly conserved proteins that contribute to proper folding by shielding folding proteins from other proteins that could hinder the process. Proper protein folding is one of the main prerequisites for post-translational modifications. Incorrect folding, if not dealt with, can lead to a buildup of protein misfoldings that damage cells and cause widespread abnormalities. Said post-translational modifications, widespread in eukaryotes, are critical for protein structure, function and biological activity. Incorrect post-translational protein modifications may lead to individual consequences or aggregation of therapeutic proteins. In this review article, we have tried to examine some key aspects of recombinant protein expression. Accordingly, the relevance of these proteins is highlighted, major problems related to the production of recombinant protein and to refolding issues are pinpointed and suggested solutions are presented. An overview of post-translational modification, their biological significance and methods of identification are also provided. Overall, the work is expected to illustrate challenges in recombinant protein expression.
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Affiliation(s)
- Azadeh Beygmoradi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
| | - Roohullah Hemmati
- Department of Biology, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Pedro Fernandes
- DREAMS and Faculdade de Engenharia, Universidade Lusófona de Humanidades e Tecnologias, Av. Campo Grande 376, 1749-024 Lisboa, Portugal; iBB-Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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14
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Antibody-free approach for ubiquitination profiling by selectively clicking the ubiquitination sites. Anal Chim Acta 2023; 1246:340877. [PMID: 36764771 DOI: 10.1016/j.aca.2023.340877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
Abstract
Ubiquitination is a reversible post-translational modification that plays a pivotal role in numerous biological processes. Antibody-based approaches, as the most used methods for identifying ubiquitination sites, exist sequence recognition bias, high cost, and ubiquitin-like protein modification interference, limiting their widespread application. Here, we proposed an Antibody-Free approach for Ubiquitination Profiling, termed AFUP, by selectively clicking the ubiquitinated lysine to enrich and profile endogenous ubiquitinated peptides using mass spectrometry. Briefly, protein amines were blocked with formaldehyde, and then the ubiquitin molecules were hydrolyzed from the ubiquitinated proteins by non-specific deubiquitinases USP2 and USP21 to release the free ε-amine of lysine. Peptides containing free ε-amines were selectively enriched with streptavidin beads upon NHS-SS-biotin labeling. Finally, the enriched peptides were eluted by DTT and analyzed by LC-MS/MS, resulting in ubiquitination profiling. Preliminary experiment showed that 349 ± 7 ubiquitination sites were identified in 0.8 mg HeLa lysates with excellent reproducibility (CV = 2%) and high quantitative stability (Pearson, r ≥ 0.91) using our method. With the combination of AFUP and simple basic C18 pre-fractionation, approximately 4000 ubiquitination sites were identified in a single run of 293T cells. In addition, we showed that 209 ubiquitination sites were significantly regulated in UBE2O knockdown cells after normalized to protein abundance. In conclusion, our results demonstrated that AFUP is a robust alternative strategy for ubiquitomics research.
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15
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Nakagawa H, Higurashi M, Ishikawa F, Mori K, Shibanuma M. An indispensable role of TAZ in anoikis resistance promoted by OTUB1 deubiquitinating enzyme in basal-like triple-negative breast cancer cells. Biochem Biophys Res Commun 2023; 649:1-9. [PMID: 36738577 DOI: 10.1016/j.bbrc.2023.01.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/25/2023] [Indexed: 01/27/2023]
Abstract
Aggressive cancers, such as triple-negative breast cancer (TNBC), are mostly fatal because of their potential to metastasize to distant organs. Cancer cells acquire various abilities to metastasize, including resistance to anoikis, an apoptotic cell death induced by loss of anchorage to the extracellular matrix. Transcriptional coactivator with PDZ binding motif (TAZ) and Yes-associated protein (YAP), the downstream effectors of the Hippo pathway, regulate cell- and tissue-level architectures by responding to mechanical microenvironments of cells, including the cell-extracellular matrix interaction. The Hippo pathway is frequently disrupted in cancer cells, and TAZ and YAP are irrelevantly activated, potentially resulting in anchorage-independent survival/proliferation of cancer cells and metastatic progression. The study aims to investigate the roles of TAZ and YAP in anoikis resistance in basal-like (BL) TNBC cells, which comprise a major subtype (>70%) of TNBC. We found that TAZ and YAP had nonredundant roles in anchorage-independent cancer cell survival or anoikis resistance. Particularly, TAZ was indispensable for anoikis resistance in BL-TNBC cells but not for survival of non-transformed mammary epithelial cells (MECs). In contrast, YAP, a paralog of TAZ, was indispensable for survival of both non-transformed MECs and cancer cells. Therefore, TAZ might be a preferable therapeutic target against dissemination of aggressive cancer cells without killing normal cells. Interestingly, TAZ was abnormally stabilized in BL-TNBC cells under non-adherent conditions, which promoted anoikis resistance. Furthermore, OTUB1, a deubiquitinating enzyme, was responsible for the stabilization of TAZ in detached BL-TNBC cells. Importantly, simultaneous high expression of TAZ and OTUB1 was associated with poor prognosis in BC. Thus, OTUB1 has emerged as a potentially druggable target. Successful inhibition of OTUB1 enzymatic activity is expected to downregulate TAZ and eventually prevents metastasis of aggressive cancers, such as BL-TNBC.
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Affiliation(s)
- Hidetsugu Nakagawa
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, Japan
| | - Masato Higurashi
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, Japan
| | - Fumihiro Ishikawa
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, Japan
| | - Kazunori Mori
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, Japan.
| | - Motoko Shibanuma
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, Japan
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16
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Carmon H, Haley EC, Parikh V, Tronson NC, Sarter M. Neuro-Immune Modulation of Cholinergic Signaling in an Addiction Vulnerability Trait. eNeuro 2023; 10:ENEURO.0023-23.2023. [PMID: 36810148 PMCID: PMC9997697 DOI: 10.1523/eneuro.0023-23.2023] [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: 01/20/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023] Open
Abstract
Sign-tracking (ST) describes the propensity to approach and contact a Pavlovian reward cue. By contrast, goal-trackers (GTs) respond to such a cue by retrieving the reward. These behaviors index the presence of opponent cognitive-motivational traits, with STs exhibiting attentional control deficits, behavior dominated by incentive motivational processes, and vulnerability for addictive drug taking. Attentional control deficits in STs were previously attributed to attenuated cholinergic signaling, resulting from deficient translocation of intracellular choline transporters (CHTs) into synaptosomal plasma membrane. Here, we investigated a posttranslational modification of CHTs, poly-ubiquitination, and tested the hypothesis that elevated cytokine signaling in STs contributes to CHT modification. We demonstrated that intracellular CHTs, but not plasma membrane CHTs, are highly ubiquitinated in male and female sign-tracking rats when compared with GTs. Moreover, levels of cytokines measured in cortex and striatum, but not spleen, were higher in STs than in GTs. Activation of the innate immune system by systemic administration of the bacterial endotoxin lipopolysaccharide (LPS) elevated ubiquitinated CHT levels in cortex and striatum of GTs only, suggesting ceiling effects in STs. In spleen, LPS increased levels of most cytokines in both phenotypes. In cortex, LPS particularly robustly increased levels of the chemokines CCL2 and CXCL10. Phenotype-specific increases were restricted to GTs, again suggesting ceiling effects in STs. These results indicate that interactions between elevated brain immune modulator signaling and CHT regulation are essential components of the neuronal underpinnings of the addiction vulnerability trait indexed by sign-tracking.
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Affiliation(s)
- Hanna Carmon
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109
| | - Evan C Haley
- Department of Psychology and Neuroscience, Temple University, Philadelphia, PA 19122
| | - Vinay Parikh
- Department of Psychology and Neuroscience, Temple University, Philadelphia, PA 19122
| | - Natalie C Tronson
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109
- Department of Psychology and Neuroscience Program, University of Michigan, Ann Arbor, MI 48109
| | - Martin Sarter
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109
- Department of Psychology and Neuroscience Program, University of Michigan, Ann Arbor, MI 48109
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17
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Bhattacharjee D, Kaveti S, Jain N. APC/C CDH1 ubiquitinates STAT3 in mitosis. Int J Biochem Cell Biol 2023; 154:106333. [PMID: 36400381 DOI: 10.1016/j.biocel.2022.106333] [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: 06/30/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
STAT3, an oncogene drives tumor growth and is associated with poor prognosis. However, small molecule-based STAT3 inhibitors were unsuccessful in clinics. Recently, STAT3 degraders that ubiquitinate STAT3 were found to elicit long-lasting anti-tumor responses. Thus, triggering STAT3 ubiquitination in cancers is a better strategy than STAT3 inhibition. However, not much is known about the identity of E3-ligases that ubiquitinate STAT3 in cancers. Therefore, to design better therapies to degrade STAT3, we sought to identify E3-ligases that ubiquitinate STAT3 in cancer cells. To answer this question, we determined the cell cycle-dependent ubiquitination of STAT3 in HEK293T cells and examined the link between STAT3 dephosphorylation and ubiquitination. We found that STAT3 is more strongly ubiquitinated in mitosis than in other phases of the cell cycle. We observed that APC/C CDH1 binds and ubiquitinates STAT3 in mitosis. Further, we also found that inhibiting phosphatases decreases STAT3 ubiquitination. We conclude that APC/C CDH1 ubiquitinates STAT3 in mitosis. We suggest that mitosis can be a potential therapeutic window for treating STAT3-activated cancers.
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Affiliation(s)
- Debanjan Bhattacharjee
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Sreeram Kaveti
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India.
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18
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A Truncated Form of the p27 Cyclin-Dependent Kinase Inhibitor Translated from Pre-mRNA Causes G 2-Phase Arrest. Mol Cell Biol 2022; 42:e0021722. [PMID: 36317925 PMCID: PMC9671031 DOI: 10.1128/mcb.00217-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-mRNA splicing is an indispensable mechanism for eukaryotic gene expression. Splicing inhibition causes cell cycle arrest at the G1 and G2/M phases, and this is thought to be one of the reasons for the potent antitumor activity of splicing inhibitors. However, the molecular mechanisms underlying the cell cycle arrest have many unknown aspects. In particular, the mechanism of G2/M-phase arrest caused by splicing inhibition is completely unknown. Here, we found that lower and higher concentrations of pladienolide B caused M-phase and G2-phase arrest, respectively. We analyzed protein levels of cell cycle regulators and found that a truncated form of the p27 cyclin-dependent kinase inhibitor, named p27*, accumulated in G2-arrested cells. Overexpression of p27* caused partial G2-phase arrest. Conversely, knockdown of p27* accelerated exit from G2/M phase after washout of splicing inhibitor. These results suggest that p27* contributes to G2/M-phase arrest caused by splicing inhibition. We also found that p27* bound to and inhibited M-phase cyclins, although it is well known that p27 regulates the G1/S transition. Intriguingly, p27*, but not full-length p27, was resistant to proteasomal degradation and remained in G2/M phase. These results suggest that p27*, which is a very stable truncated protein in G2/M phase, contributes to G2-phase arrest caused by splicing inhibition.
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19
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Wittorf KJ, Weber KK, Swenson SA, Buckley SM. Ubiquitin E3 ligase FBXO21 regulates cytokine-mediated signaling pathways, but is dispensable for steady-state hematopoiesis. Exp Hematol 2022; 114:33-42.e3. [PMID: 35987460 DOI: 10.1016/j.exphem.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]
Abstract
Hematopoietic cell fate decisions such as self-renewal and differentiation are highly regulated through multiple molecular pathways. One pathway, the ubiquitin proteasome system (UPS), controls protein levels by tagging them with polyubiquitin chains and promoting their degradation through the proteasome. Ubiquitin E3 ligases serve as the substrate-recognition component of the UPS. By investigating the FBOX family of E3 ligases, we discovered that Fbxo21 was highly expressed in the hematopoietic stem and progenitor cell (HSPC) population, and exhibited low to no expression in mature myeloid populations. To determine the role of FBXO21 on HSPC maintenance, self-renewal, and differentiation, we generated shRNAs against FBXO21 and a hematopoiesis-specific Fbxo21 conditional knockout (cKO) mouse model. We found that silencing FBXO21 in HSPCs led to a loss in colony formation and an increase in cell differentiation in vitro. Additionally, stressing the HSPC populations in our Fbxo21 cKO mouse with 5-fluorouracil injections resulted in a decrease in survival, despite these populations exhibiting minimal alterations during steady-state hematopoiesis. Although FBXO21 has previously been proposed to regulate cytokine signaling via ASK and p38, our results indicate that depletion of FBXO21 led to altered ERK signaling in vitro. Together, these findings suggest ubiquitin E3 ligase FBXO21 regulates HSPCs through cytokine-mediated pathways.
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Affiliation(s)
- Karli J Wittorf
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Kasidy K Weber
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Samantha A Swenson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Shannon M Buckley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE.
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20
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Maruyama T, Saito K, Higurashi M, Ishikawa F, Kohno Y, Mori K, Shibanuma M. HMGA2 drives the IGFBP1/AKT pathway to counteract the increase in P27KIP1 protein levels in mtDNA/RNA-less cancer cells. Cancer Sci 2022; 114:152-163. [PMID: 36102493 PMCID: PMC9807519 DOI: 10.1111/cas.15582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/06/2022] [Accepted: 09/02/2022] [Indexed: 01/07/2023] Open
Abstract
Recent comprehensive analyses of mtDNA and orthogonal RNA-sequencing data revealed that in numerous human cancers, mtDNA copy numbers and mtRNA amounts are significantly reduced, followed by low respiratory gene expression. Under such conditions (called mt-Low), cells encounter severe cell proliferation defects; therefore, they must acquire countermeasures against this fatal disadvantage during malignant transformation. This study elucidated a countermeasure against the mt-Low condition-induced antiproliferative effects in hepatocellular carcinoma (HCC) cells. The mechanism relied on the architectural transcriptional regulator HMGA2, which was preferably expressed in HCC cells of the mt-Low type in vitro and in vivo. Detailed in vitro analyses suggest that HMGA2 regulates insulin-like growth factor binding protein 1 (IGFBP1) expression, leading to AKT activation, which then phosphorylates the cyclin-dependent kinase inhibitor (CKI), P27KIP1, and facilitates its ubiquitin-mediated degradation. Accordingly, intervention in the HMGA2 function by RNAi resulted in an increase in P27KIP1 levels and an induction of senescence-like cell proliferation inhibition in mt-Low-type HCC cells. Conclusively, the HMGA2/IGFBP1/AKT axis has emerged as a countermeasure against P27KIP1 CKI upregulation under mt-Low conditions, thereby circumventing cell proliferation inhibition and supporting the tumorigenic state. Notably, similar to in vitro cell lines, HMGA2 was likely to regulate IGFBP1 expression in HCC in vivo, thereby contributing to poor patient prognosis. Considering the significant number of cases under mt-Low or the threat of CKI upregulation cancer-wide, the axis is noteworthy as a vulnerability of cancer cells or target for tumor-agnostic therapy inducing irreversible cell proliferation inhibition via CKI upregulation in a large population with cancer.
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Affiliation(s)
- Tsuyoshi Maruyama
- Division of Cancer Cell Biology, Department of Pharmaceutical SciencesShowa University School of PharmacyTokyoJapan
| | - Koji Saito
- Department of PathologyShowa University School of MedicineTokyoJapan,Department of PathologyTeikyo University HospitalTokyoJapan
| | - Masato Higurashi
- Division of Cancer Cell Biology, Department of Pharmaceutical SciencesShowa University School of PharmacyTokyoJapan
| | - Fumihiro Ishikawa
- Division of Cancer Cell Biology, Department of Pharmaceutical SciencesShowa University School of PharmacyTokyoJapan
| | - Yohko Kohno
- Showa University Koto Toyosu HospitalTokyoJapan
| | - Kazunori Mori
- Division of Cancer Cell Biology, Department of Pharmaceutical SciencesShowa University School of PharmacyTokyoJapan
| | - Motoko Shibanuma
- Division of Cancer Cell Biology, Department of Pharmaceutical SciencesShowa University School of PharmacyTokyoJapan
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21
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Teranishi H, Tabata K, Saeki M, Umemoto T, Hatta T, Otomo T, Yamamoto K, Natsume T, Yoshimori T, Hamasaki M. Identification of CUL4A-DDB1-WDFY1 as an E3 ubiquitin ligase complex involved in initiation of lysophagy. Cell Rep 2022; 40:111349. [PMID: 36103833 DOI: 10.1016/j.celrep.2022.111349] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023] Open
Abstract
Macroautophagy is a bulk degradation system in which double membrane-bound structures called autophagosomes to deliver cytosolic materials to lysosomes. Autophagy promotes cellular homeostasis by selectively recognizing and sequestering specific targets, such as damaged organelles, protein aggregates, and invading bacteria, termed selective autophagy. We previously reported a type of selective autophagy, lysophagy, which helps clear damaged lysosomes. Damaged lysosomes become ubiquitinated and recruit autophagic machinery. Proteomic studies using transfection reagent-coated beads and further evaluations reveal that a CUL4A-DDB1-WDFY1 E3 ubiquitin ligase complex is essential to initiate lysophagy and clear damaged lysosomes. Moreover, we show that LAMP2 is ubiquitinated by the CUL4A E3 ligase complex as a substrate on damaged lysosomes. These results reveal how cells selectively tag damaged lysosomes to initiate autophagy for the clearance of lysosomes.
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Affiliation(s)
- Hirofumi Teranishi
- JT Pharmaceutical Frontier Research Laboratory, Yokohama 236-0004, Japan
| | - Keisuke Tabata
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan
| | - Marika Saeki
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Tetsuo Umemoto
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, AIST, Tokyo 135-0064, Japan
| | - Takanobu Otomo
- Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Toru Natsume
- Molecular Profiling Research Center for Drug Discovery, AIST, Tokyo 135-0064, Japan
| | - Tamotsu Yoshimori
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan.
| | - Maho Hamasaki
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan.
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22
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Sun M, Zhang X. Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture. Cell Biosci 2022; 12:126. [PMID: 35962460 PMCID: PMC9373315 DOI: 10.1186/s13578-022-00870-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification (PTM), which regulates diverse fundamental features of protein substrates, including stability, activity, and localization. Unsurprisingly, dysregulation of the complex interaction between ubiquitination and deubiquitination leads to many pathologies, such as cancer and neurodegenerative diseases. The versatility of ubiquitination is a result of the complexity of ubiquitin (Ub) conjugates, ranging from a single Ub monomer to Ub polymers with different length and linkage types. To further understand the molecular mechanism of ubiquitination signaling, innovative strategies are needed to characterize the ubiquitination sites, the linkage type, and the length of Ub chain. With advances in chemical biology tools, computational methodologies, and mass spectrometry, protein ubiquitination sites and their Ub chain architecture have been extensively revealed. The obtained information on protein ubiquitination helps to crack the molecular mechanism of ubiquitination in numerous pathologies. In this review, we summarize the recent advances in protein ubiquitination analysis to gain updated knowledge in this field. In addition, the current and future challenges and barriers are also reviewed and discussed.
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23
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Zhang M, Berk JM, Mehrtash AB, Kanyo J, Hochstrasser M. A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins. PLoS Biol 2022; 20:e3001501. [PMID: 35771886 PMCID: PMC9278747 DOI: 10.1371/journal.pbio.3001501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/13/2022] [Accepted: 05/30/2022] [Indexed: 01/07/2023] Open
Abstract
Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites. This study presents OtUBD, a new tool derived from a bacterial deubiquitylase, for the purification and analysis of a broad range of endogenous ubiquitylated proteins, including monoubiquitylation, polyubiquitylation, non-lysine ubiquitylation and potentially other macromolecules.
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Affiliation(s)
- Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jason M. Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Adrian B. Mehrtash
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jean Kanyo
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, United States of America
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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24
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Saikiran Reddy M, Bhattacharjee D, Jain N. Plk1 regulates mutant IDH1 enzyme activity and mutant IDH2 ubiquitination in mitosis. Cell Signal 2022; 92:110279. [PMID: 35143931 DOI: 10.1016/j.cellsig.2022.110279] [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: 09/16/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
Abstract
Mutations in the metabolic enzymes, IDH1 and IDH2 are frequently found in glioma, chondrosarcoma, and acute myeloid leukemia. In our previous study, we showed that mutant IDH1 and IDH2 proteins levels are high in mitosis, and mutant IDH1 enzyme activity increases in mitosis. In another study, we observed that mutant IDH2 is ubiquitinated in mitosis in an APC/C-dependent manner. To orchestrate mitosis, kinases phosphorylate key proteins and regulate their functions. But it is unknown, whether mitotic kinases regulate mutant IDH1 and IDH2. As IDH1 and IDH2 have 66% sequence identity, thus we hypothesized that a common mitotic kinase(s) may regulate mutant IDH1 and IDH2 in mitosis. To test our hypothesis, we examined mutant IDH1 and IDH2 binding to mitotic kinases and determined their role in regulating mutant IDH1 and IDH2 in mitosis. Here, we observed that Cdk1/Cyclin B1 phosphorylated mutant IDH1 and IDH2 binds Plk1. Conserved Plk1 phosphobinding sites in IDH1 and IDH2 are important for Plk1 binding. We found that Plk1 regulates mutant IDH1 enzyme activity and blocking Plk1 decreases D-2HG, whereas, overexpressing Plk1 increases D-2HG levels. Furthermore, blocking Plk1 decreases mutant IDH2 ubiquitination, whereas, overexpressing Plk1 increases mutant IDH2 ubiquitination in mitosis. We conclude that Plk1 regulates mutant IDH1 enzyme activity and mutant IDH2 ubiquitination in mitosis. Based on our results, we suggest that Plk1 can be a therapeutic target in mutant IDH-linked tumours.
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Affiliation(s)
- M Saikiran Reddy
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debanjan Bhattacharjee
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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25
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Lord SO, Lai Y. Exercise mediates ubiquitin signalling in human skeletal muscle. FASEB Bioadv 2022; 4:402-407. [PMID: 35664833 PMCID: PMC9164242 DOI: 10.1096/fba.2021-00142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Physical activity or regular exercise provides many beneficial effects towards human health, helping prevent and ameliorate metabolic diseases. However, certain molecular mechanisms that mediate these health benefits remain poorly understood. Parker et al. provided the first global analysis of exercise‐regulated ubiquitin signalling in human skeletal muscle, revealing post‐translational modification cross‐talk. As a result of their analysis, NEDDylation is thought to promote ubiquitin signalling for the removal of damaged proteins following exercise. The proteomic dataset generated from their study is invaluable for researchers in this field to validate new mechanistic hypotheses. To further reveal molecular mechanisms regulated by exercise, future research could employ more sensitive mass spectrometry‐based workflows that increase the detection of both ubiquitylated sites and peptides and subsequently identify more exercise‐regulated ubiquitin signalling pathways.
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Affiliation(s)
- Samuel O. Lord
- School of Sport, Exercise and Rehabilitation Sciences University of Birmingham Birmingham United Kingdom
| | - Yu‐Chiang Lai
- School of Sport, Exercise and Rehabilitation Sciences University of Birmingham Birmingham United Kingdom
- Institute of Metabolism and Systems Research University of Birmingham Birmingham United Kingdom
- Mitochondrial Profiling Centre University of Birmingham Birmingham United Kingdom
- Medical Research Council (MRC) Versus Arthritis Centre for Musculoskeletal Ageing Research University of Birmingham Birmingham United Kingdom
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26
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Villamil M, Xiao W, Yu C, Huang L, Xu P, Kaiser P. The Ubiquitin Interacting Motif-Like Domain of Met4 Selectively Binds K48 Polyubiquitin Chains. Mol Cell Proteomics 2022; 21:100175. [PMID: 34763062 PMCID: PMC8693465 DOI: 10.1016/j.mcpro.2021.100175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 10/13/2021] [Accepted: 11/05/2021] [Indexed: 11/20/2022] Open
Abstract
Protein ubiquitylation is an important posttranslational modification that governs most cellular processes. Signaling functions of ubiquitylation are very diverse and involve proteolytic as well as nonproteolytic events, such as localization, regulation of protein interactions, and control of protein activity. The intricacy of ubiquitin signaling is further complicated by several different polyubiquitin chain types that are likely recognized and interpreted by different protein readers. For example, K48-linked ubiquitin chains represent the most abundant chain topology and are the canonical degradation signals, but have been implicated in degradation-independent functions as well, likely requiring a variety of protein readers. Ubiquitin binding domains that interact with polyubiquitin chains are likely at the center of ubiquitin signal recognition and transmission, but their structure and selectivity are largely unexplored. Here we report identification and characterization of the ubiquitin interacting motif-like (UIML) domain of the yeast transcription factor Met4 as a strictly K48-polyubiquitin specific binding unit using methods such as biolayer interferometry (BLI), pull-down assays, and mass spectrometry. We further used the selective binding property to develop an affinity probe for purification of proteins modified with K48-linked polyubiquitin chains. The affinity probe has a Kd = 100 nM for K48 tetra-ubiquitin and shows no detectable interaction with either monoubiquitin or any other polyubiquitin chain configuration. Our results define a short strictly K48-linkage-dependent binding motif and present a new affinity reagent for the K48-polyubiquitin-modified proteome. Our findings benefit the ubiquitin field in analyses of the role of K48-linked polyubiquitylation and increase our understanding of chain topology selective ubiquitin chain recognition.
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Affiliation(s)
- Mark Villamil
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Clinton Yu
- Department of Physiology & Biophysics, University of California Irvine, Irvine, California, USA
| | - Lan Huang
- Department of Physiology & Biophysics, University of California Irvine, Irvine, California, USA
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA.
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27
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Ultra-sensitive techniques for detecting neurological biomarkers: Prospects for early diagnosis. Biochem Biophys Res Commun 2021; 584:15-18. [PMID: 34753063 DOI: 10.1016/j.bbrc.2021.10.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/29/2021] [Indexed: 01/26/2023]
Abstract
Identifying reliable biomarkers and ultra-sensitive techniques are crucial for the early detection of neurodegenerative disorders (NDDs) to improve the clinical diagnosis and development of effective disease-modifying treatments. Here, we discussed recent technological advancements that enabled scientists to monitor brain health by detecting biological molecules even at lower levels. These technologies enabled the detection of neurological biomarkers in blood, revolutionizing the diagnosis and prognosis of NDDs. Moreover, it provided a better understanding of disease pathology's long-term effects, resulting in fewer invasive tests, early diagnosis, faster drug development, and possibly more effective therapies as possible outcomes.
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28
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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29
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Wang P, Nolan TM, Clark NM, Jiang H, Montes-Serey C, Guo H, Bassham DC, Walley JW, Yin Y. The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis. THE PLANT CELL 2021; 33:3532-3554. [PMID: 34436598 PMCID: PMC8566207 DOI: 10.1093/plcell/koab210] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/14/2021] [Indexed: 05/02/2023]
Abstract
Brassinosteroids (BRs) regulate plant growth, development, and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1), whose degradation occurs through the proteasome and autophagy pathways. The E3 ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. Here, we identified an F-box family E3 ubiquitin ligase named BES1-ASSOCIATED F-BOX1 (BAF1) in Arabidopsis thaliana. BAF1 interacts with BES1 and mediates its ubiquitination and degradation. Our genetic data demonstrated that BAF1 inhibits BR signaling in a BES1-dependent manner. Moreover, BAF1 targets BES1 for autophagic degradation in a selective manner. BAF1-triggered selective autophagy of BES1 depends on the ubiquitin binding receptor DOMINANT SUPPRESSOR OF KAR2 (DSK2). Sucrose starvation-induced selective autophagy of BES1, but not bulk autophagy, was significantly compromised in baf1 mutant and BAF1-ΔF (BAF1 F-box decoy) overexpression plants, but clearly increased by BAF1 overexpression. The baf1 and BAF1-ΔF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as an E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Hao Jiang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | | | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011
- Author for correspondence:
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30
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Yokoyama A, Kouketsu T, Otsubo Y, Noro E, Sawatsubashi S, Shima H, Satoh I, Kawamura S, Suzuki T, Igarashi K, Sugawara A. Identification and Functional Characterization of a Novel Androgen Receptor Coregulator, EAP1. J Endocr Soc 2021; 5:bvab150. [PMID: 34585037 PMCID: PMC8462380 DOI: 10.1210/jendso/bvab150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
The androgen receptor (AR) plays an essential role in the development of prostate cancer, and androgen-deprivation therapy is used as a first-line treatment for prostate cancer. However, under androgen-deprivation therapy, castration-resistant prostate cancer inevitably arises, suggesting that the interacting transcriptional coregulators of AR are promising targets for developing novel therapeutics. In this study, we used novel proteomic techniques to evaluate the AR interactome, including biochemically labile binding proteins, which might go undetected by conventional purification methods. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, we identified enhanced at puberty 1 (EAP1) as a novel AR coregulator, whereas its interaction with AR could not be detected under standard biochemical conditions. EAP1 enhanced the transcriptional activity of AR via the E3 ubiquitin ligase activity, and its ubiquitination substrate proteins included AR and HDAC1. Furthermore, in prostate cancer specimens, EAP1 expression was significantly correlated with AR expression as well as a poor prognosis of prostate cancer. Together, these results suggest that EAP1 is a novel AR coregulator that promotes AR activity and potentially plays a role in prostate cancer progression.
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Affiliation(s)
- Atsushi Yokoyama
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Takumi Kouketsu
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Yuri Otsubo
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Erika Noro
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Shun Sawatsubashi
- Department of Molecular Endocrinology, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Ikuro Satoh
- Department of Pathology, Miyagi Cancer Center, Natori, Miyagi 981-1293, Japan
| | - Sadafumi Kawamura
- Department of Urology, Miyagi Cancer Center, Natori, Miyagi 981-1293, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Akira Sugawara
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
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31
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Fuchs SY, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J Virol 2021; 95:e0086221. [PMID: 34260266 PMCID: PMC8428404 DOI: 10.1128/jvi.00862-21] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectible human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectible human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Brianna J. Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Raghuveera K. Goel
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Benjamin Blum
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Alexander H. Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hasahn L. Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Vipul C. Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Boston Veterans Affairs Healthcare System, Boston, Massachusetts, USA
- Institute of Medical Engineering and Sciences, MA Institute of Technology, Cambridge, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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32
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Lambhate S, Bhattacharjee D, Jain N. APC/C CDH1 ubiquitinates IDH2 contributing to ROS increase in mitosis. Cell Signal 2021; 86:110087. [PMID: 34271087 DOI: 10.1016/j.cellsig.2021.110087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022]
Abstract
NADPH is a cofactor used by reactive oxygen species (ROS) scavenging enzymes to block ROS produced in cells. Recently, it was shown that in cancer cells, ROS progressively increases in tune to cell cycle leading to a peak in mitosis. Loss of IDH2 is known to cause severe oxidative stress in cell and mouse models as ROS increases in mitochondria. Therefore, we hypothesized that IDH2, a major NADPH-producing enzyme in mitochondria is ubiquitinated for ROS to increase in mitosis. To test this hypothesis, in cancer cells we examined IDH2 ubiquitination in mitosis and measured the ROS produced. We found that IDH2 is ubiquitinated in mitosis and on inhibiting anaphase-promoting complex/Cyclosome (APC/C) IDH2 was stabilized. Further, we observed that overexpressing APC/C coactivator CDH1 decreased IDH2, whereas depleting CDH1 decreased IDH2 ubiquitination. To understand the link between IDH2 ubiquitination and ROS produced in mitosis, we show that overexpressing mitochondria-targeted-IDH1 decreased ROS by increasing NADPH in IDH2 ubiquitinated cells. We conclude that APC/C CDH1 ubiquitinates IDH2, a major NADPH-producing enzyme in mitochondria contributing to ROS increase in mitosis. Based on our results, we suggest that mitosis can be a therapeutic window in mutant IDH2-linked pathologies.
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Affiliation(s)
- Surbhi Lambhate
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debanjan Bhattacharjee
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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33
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Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
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Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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34
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Yasukawa T, Tsutsui A, Tomomori-Sato C, Sato S, Saraf A, Washburn MP, Florens L, Terada T, Shimizu K, Conaway RC, Conaway JW, Aso T. NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation. Cell Rep 2021; 30:3478-3491.e6. [PMID: 32160551 DOI: 10.1016/j.celrep.2020.02.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 12/09/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease caused by accumulations of Aβ peptides. Production and fibrillation of Aβ are downregulated by BRI2 and BRI3, which are physiological inhibitors of amyloid precursor protein (APP) processing and Aβ oligomerization. Here, we identify nuclear receptor binding protein 1 (NRBP1) as a substrate receptor of a Cullin-RING ubiquitin ligase (CRL) that targets BRI2 and BRI3 for degradation. Moreover, we demonstrate that (1) dimerized NRBP1 assembles into a functional Cul2- and Cul4A-containing heterodimeric CRL through its BC-box and an overlapping cryptic H-box, (2) both Cul2 and Cul4A contribute to NRBP1 CRL function, and (3) formation of the NRBP1 heterodimeric CRL is strongly enhanced by chaperone-like function of TSC22D3 and TSC22D4. NRBP1 knockdown in neuronal cells results in an increase in the abundance of BRI2 and BRI3 and significantly reduces Aβ production. Thus, disrupting interactions between NRBP1 and its substrates BRI2 and BRI3 may provide a useful therapeutic strategy for AD.
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Affiliation(s)
- Takashi Yasukawa
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Aya Tsutsui
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | | | - Shigeo Sato
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tohru Terada
- Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Teijiro Aso
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan.
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35
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Lin Z, Miao J, Zhang T, He M, Wang Z, Feng X, Bai L. JUNB-FBXO21-ERK axis promotes cartilage degeneration in osteoarthritis by inhibiting autophagy. Aging Cell 2021; 20:e13306. [PMID: 33450132 PMCID: PMC7884044 DOI: 10.1111/acel.13306] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 01/22/2023] Open
Abstract
Osteoarthritis (OA) is a heterogeneous disease that is extremely hard to cure owing to its complex regulation network of pathogenesis, especially cartilage degeneration. FBXO21 is a subunit of ubiquitin E3 ligases that degrades P-glycoprotein and EID1 by ubiquitination and activates the JNK and p38 pathways; however, its role in OA remains unknown. Here, the main objective of this study was to evaluate the potential effects and mechanism of FBXO21 in OA degeneration, we revealed that FBXO21 is upregulated in the cartilage of patients with OA, aging, and monosodium iodoacetate-induced OA rats, and chondrocytes treated with interleukin-1β, tumor necrosis factor-α, and lipopolysaccharide. Moreover, the in vivo and in vitro knockdown of FBXO21 suppressed OA-related cartilage degeneration, as evidenced by activated autophagy, upregulated anabolism, alleviated apoptosis, and downregulated catabolism. In contrast, its overexpression promoted OA-related cartilage degeneration. In addition, using mass spectrometry and co-immunoprecipitation assay, we demonstrated that the downstream mechanism of FBXO21 inhibits autophagy by interacting with and phosphorylating ERK. Furthermore, FBXO21 alleviated anabolism and enhanced apoptosis and catabolism by inhibiting autophagy in rat chondrocytes. Interestingly, for its upstream mechanism, JUNB promoted FBXO21 expression by directly targeting the FBXO21 promoter, thus further accelerating cartilage degeneration in SW1353 cells and rat chondrocytes. Overall, our findings reveal that the JUNB-FBXO21-ERK axis regulates OA apoptosis and cartilage matrix metabolism by inhibiting autophagy. Therefore, FBXO21 is an attractive target for regulating OA pathogenesis, and its knockdown may provide a novel targeted therapy for OA.
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Affiliation(s)
- Zhiming Lin
- Department of Orthopedics Shengjing Hospital of China Medical University Shenyang China
| | - Jianing Miao
- Medical Research Center/Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases Shenyang China
| | - Tao Zhang
- Department of Thoracic Surgery Xiamen Branch of Zhongshan Hospital of Fudan University Xiamen China
| | - Ming He
- Department of Orthopedics Shengjing Hospital of China Medical University Shenyang China
| | - Ziyuan Wang
- Department of Orthopedics Shengjing Hospital of China Medical University Shenyang China
| | - Xinyuan Feng
- Department of Orthopedics Shengjing Hospital of China Medical University Shenyang China
| | - Lunhao Bai
- Department of Orthopedics Shengjing Hospital of China Medical University Shenyang China
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36
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Wang J, Wang F, Li Q, Wang Q, Li J, Wang Y, Sun J, Lu D, Zhou H, Li S, Ma S, Xie J, Wen T. Proteomics and molecular network analyses reveal that the interaction between the TAT-DCF1 peptide and TAF6 induces an antitumor effect in glioma cells. Mol Omics 2021; 16:73-82. [PMID: 31899468 DOI: 10.1039/c9mo00068b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glioblastoma is the most lethal brain cancer in adults. Despite advances in surgical techniques, radiotherapy, and chemotherapy, their therapeutic effect is far from significant, since the detailed underlying pathological mechanism of this cancer is unclear. The establishment of molecular interaction networks has laid the foundation for the exploration of these mechanisms with a view to improving therapy for glioblastoma. In the present study, to further explore the cellular role of DCF1 (dendritic cell-derived factor 1), the proteins bound to TAT-DCF1 (transactivator of transcription-dendritic cell-derived factor 1) were identified, and biosystem analysis was employed. Functional enrichment analyses indicate that TAT-DCF1 induced important biological changes in U251 cells. Furthermore, the established molecular interaction networks indicated that TAT-DCF1 directly interacted with TAF6 in glioma cells and with UBC in HEK293T (human embryonic kidney 293T) cells. In addition, further biological experiments demonstrate that TAT-DCF1 induced the activation of the RPS27A/TOP2A/HMGB2/BCL-2 signaling pathway via interaction with TAF6 in U251 cells. Taken together, these findings suggest that the TAT-DCF1 peptide possesses great potential for the development of glioblastoma therapy through the interaction with TAF6-related pathways and provides further theoretic evidence for the mechanisms underlying the antitumor effects of TAT-DCF1.
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Affiliation(s)
- Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, 99 Shang Da Road, Shanghai 200444, China.
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37
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Jiang Y, Liu X, Shen R, Gu X, Qian W. Fbxo21 regulates the epithelial-to-mesenchymal transition through ubiquitination of Nr2f2 in gastric cancer. J Cancer 2021; 12:1421-1430. [PMID: 33531987 PMCID: PMC7847638 DOI: 10.7150/jca.49674] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
F-box protein 21 (Fbxo21), a member of the F-box family proteins, constitutes one of the four subunits of an E3 ubiquitin ligase complex called SCFs (SKP1-Cullin-F-box). Despite the effect on antivirus immune response and ubiquitination regulation of a few oncoproteins, such as EID1 and P-gp, little is known about the Fbxo21 function in tumors, including gastric cancer. In our study, we confirmed that Fbxo21 expression was decreased in gastric cancer tissues. Decreased expression of Fbxo21 was significantly associated with poor prognosis in gastric cancer. Fbxo21 inhibited gastric cancer progression by inducing growth arrest and inhibiting migration and invasion. The expression of various EMT markers, such as E-cadherin, N-cadherin and Vimentin were altered after Fbxo21 knockdown or overexpression. Moreover, we demonstrated that Fbxo21 inhibited the EMT via the down-regulation of Nr2f2. Fbxo21 expression was negatively correlated with Nr2f2 protein expression in gastric cancer tissues and cell lines. And the Nr2f2 protein abundance was regulated by Fbxo21 via ubiquitination and proteasomal degradation. At last, we demonstrated the effects of Nr2f2 re-expression and inhibition on stable Fbxo21-overexpression or Fbxo21-silenced cell lines. These results suggested that Fbxo21 inhibited the proliferation and EMT in part through down-regulating the Nr2f2.
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Affiliation(s)
- Yannan Jiang
- Department of General Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University
| | - Xinyu Liu
- Department of General Surgery, The First Affiliated Hospital of Zhengzhou University
| | - Renbin Shen
- Department of General Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University
| | - Xinhua Gu
- Department of General Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University
| | - Weifeng Qian
- Department of General Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University
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38
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ZHONG H, HUANG Y, JIN Y, ZHAO R. [Advances in the application of affinity separation for analyzing protein ubiquitination]. Se Pu 2021; 39:26-33. [PMID: 34227356 PMCID: PMC9274849 DOI: 10.3724/sp.j.1123.2020.07005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Indexed: 11/25/2022] Open
Abstract
Protein ubiquitination is one of the most common yet complex post-translational modifications in eukaryotes that plays an important role in various biological processes including cell signal transduction, growth, and metabolism. Disorders in the ubiquitination process have been revealed to correlate with the occurrence and development of many diseases such as neurodegenerative disease, inflammation, and cancer. Investigation of protein ubiquitination is of great importance to uncover protein functions, understand the molecular mechanisms underlying biological processes, and develop novel strategies for disease treatment. Great advances have been made toward understanding protein ubiquitination; however, it remains a challenging task due to the high diversity of ubiquitination sites and structures, as well as the dynamic nature of ubiquitination in biological processes. Protein ubiquitination occurs through the formation of a covalent bond between the carboxyl terminus of ubiquitin and the ε-amino group of a lysine residue in the substrate. As a small protein, ubiquitin itself can be further modified by another ubiquitin molecule to form homotypic or heterotypic polyubiquitin chains. There are eight sites, namely seven lysine residues (K6, K11, K27, K29, K33, K48, and K63) and one N-terminal methionine (M1), in one ubiquitin molecule that can be used to form a ubiquitin dimer. The variations in modification sites, ubiquitin chain lengths, and conformations result in differences in protein sorting, cell signaling, and function. To resolve the high complexity of protein ubiquitination, new separation approaches are required. Affinity separation based on the specific recognition between biomolecules offers high selectivity and has been employed to study the structures and functions of ubiquitination. In addition, affinity ligands are central to the separation performance. Different affinity ligands have been developed and employed for the capture and enrichment of ubiquitylated proteins. Immunoaffinity separation based on antigen-antibody interactions has been one of the most classical separation methods. Antibodies against ubiquitin or different ubiquitin linkages have been developed and widely applied for the enrichment of ubiquitylated proteins or peptides. The specific capture allows the downstream identification of endogenous ubiquitination sites via mass spectrometry and thus facilitates understanding of the roles and dynamics of polyubiquitin signals. Ubiquitin-binding domains (UBDs) are a collection of modular protein domains that can interact with ubiquitin or polyubiquitin chains. Ubiquitin-associated domains, ubiquitin-interacting motifs, and ubiquitin-binding zinc finger domains are the most frequently used UBDs. Due to the moderate affinity of UBDs toward ubiquitin or ubiquitin chains, tandem ubiquitin-binding entities (TUBEs) have been engineered with high affinities (Kd in the nanomolar range) and exhibit potential as powerful tools for ubiquitination analysis. Because of their affinity and selectivity, UBDs and TUBEs have been applied for the isolation and identification of ubiquitylated targets in cancer cells and yeasts. Compared with antibodies and UBDs, peptides are smaller in size and can be facilely synthesized via chemical approaches. The modular structure of peptides allows for de novo design and screening of artificial ubiquitin affinity ligands for targeted capture of ubiquitinated proteins. Furthermore, the polyhistidine tag at the N-terminus of ubiquitin facilitates the purification of ubiquitylated substrates using immobilized metal affinity chromatography. Considering the high complexity of biosystems, strategies combining multiple affinity ligands have emerged to further improve separation efficiency and reduce background interference. Several combinations of antibodies with UBDs, antibodies with peptidyl tags, and UBDs with peptidyl tags have been developed and proven to be effective for the analysis of protein ubiquitination. These affinity-based approaches serve as important solutions for studying the structure-activity relationship of protein ubiquitination. This review highlights the applications and recent advances in affinity separation techniques for analyzing protein ubiquitination, focusing on the methods using antibodies, UBDs, peptides, and their combinations as affinity ligands. Further, their applications in the enrichment of ubiquitin-modified substrates and the identification of ubiquitination structures are introduced. Additionally, remaining challenges in affinity separation of protein ubiquitination and perspectives are discussed.
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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40
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E3 Ubiquitin Ligase APC/C Cdh1 Negatively Regulates FAH Protein Stability by Promoting Its Polyubiquitination. Int J Mol Sci 2020; 21:ijms21228719. [PMID: 33218190 PMCID: PMC7699203 DOI: 10.3390/ijms21228719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) is the last enzyme in the degradation pathway of the amino acids tyrosine and phenylalanine in mammals that catalyzes the hydrolysis of 4-fumarylacetoacetate into acetoacetate and fumarate. Mutations of the FAH gene are associated with hereditary tyrosinemia type I (HT1), resulting in reduced protein stability, misfolding, accelerated degradation and deficiency in functional proteins. Identifying E3 ligases, which are necessary for FAH protein stability and degradation, is essential. In this study, we demonstrated that the FAH protein level is elevated in liver cancer tissues compared to that in normal tissues. Further, we showed that the FAH protein undergoes 26S proteasomal degradation and its protein turnover is regulated by the anaphase-promoting complex/cyclosome-Cdh1 (APC/C)Cdh1 E3 ubiquitin ligase complex. APC/CCdh1 acts as a negative stabilizer of FAH protein by promoting FAH polyubiquitination and decreases the half-life of FAH protein. Thus, we envision that Cdh1 might be a key factor in the maintenance of FAH protein level to regulate FAH-mediated physiological functions.
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41
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Shi CY, Kingston ER, Kleaveland B, Lin DH, Stubna MW, Bartel DP. The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. Science 2020; 370:science.abc9359. [PMID: 33184237 DOI: 10.1126/science.abc9359] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread posttranscriptional gene repression. Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation. We found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase. This and other findings support a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin-proteasome pathway exposes the miRNA for degradation. Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs. These results elucidate the mechanism of TDMD and expand its inferred role in shaping miRNA levels in bilaterian animals.
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Affiliation(s)
- Charlie Y Shi
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elena R Kingston
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Kleaveland
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Daniel H Lin
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Stubna
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. .,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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42
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Wang YS, Wu KP, Jiang HK, Kurkute P, Chen RH. Branched Ubiquitination: Detection Methods, Biological Functions and Chemical Synthesis. Molecules 2020; 25:E5200. [PMID: 33182242 PMCID: PMC7664869 DOI: 10.3390/molecules25215200] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 11/16/2022] Open
Abstract
Ubiquitination is a versatile posttranslational modification that elicits signaling roles to impact on various cellular processes and disease states. The versatility is a result of the complexity of ubiquitin conjugates, ranging from a single ubiquitin monomer to polymers with different length and linkage types. Recent studies have revealed the abundant existence of branched ubiquitin chains in which one ubiquitin molecule is connected to two or more ubiquitin moieties in the same ubiquitin polymer. Compared to the homotypic ubiquitin chain, the branched chain is recognized or processed differently by readers and erasers of the ubiquitin system, respectively, resulting in a qualitative or quantitative alteration of the functional output. Furthermore, certain types of branched ubiquitination are induced by cellular stresses, implicating their important physiological role in stress adaption. In addition, the current chemical methodologies of solid phase peptide synthesis and expanding genetic code approach have been developed to synthesize different architectures of branched ubiquitin chains. The synthesized branched ubiquitin chains have shown their significance in understanding the topologies and binding partners of the branched chains. Here, we discuss the recent progresses on the detection, functional characterization and synthesis of branched ubiquitin chains as well as the future perspectives of this emerging field.
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Affiliation(s)
- Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30044, Taiwan
| | - Prashant Kurkute
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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Watanabe M, Saeki Y, Takahashi H, Ohtake F, Yoshida Y, Kasuga Y, Kondo T, Yaguchi H, Suzuki M, Ishida H, Tanaka K, Hatakeyama S. A substrate-trapping strategy to find E3 ubiquitin ligase substrates identifies Parkin and TRIM28 targets. Commun Biol 2020; 3:592. [PMID: 33082525 PMCID: PMC7576197 DOI: 10.1038/s42003-020-01328-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
The identification of true substrates of an E3 ligase is biologically important but biochemically difficult. In recent years, several techniques for identifying substrates have been developed, but these approaches cannot exclude indirect ubiquitination or have other limitations. Here we develop an E3 ligase substrate-trapping strategy by fusing a tandem ubiquitin-binding entity (TUBE) with an anti-ubiquitin remnant antibody to effectively identify ubiquitinated substrates. We apply this method to one of the RBR-type ligases, Parkin, and to one of the RING-type ligases, TRIM28, and identify previously unknown substrates for TRIM28 including cyclin A2 and TFIIB. Furthermore, we find that TRIM28 promotes cyclin A2 ubiquitination and degradation at the G1/S phase and suppresses premature entry into S phase. Taken together, the results indicate that this method is a powerful tool for comprehensively identifying substrates of E3 ligases. Watanabe et al. combine two previously developed strategies to identify E3 ubiquitin ligase substrates into a method, TR-TUBE that is subsequently used to identify substrates of the Parkin and TRIM28 ligases. They identify known substrates, validating the utility of the approach, and find that TRIM28 targets Cyclin A and TFIIB for degradation.
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Affiliation(s)
- Masashi Watanabe
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan.
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-Ku, Tokyo, 156-8506, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Fumiaki Ohtake
- Life Science Tokyo Advanced Research Center, Hoshi University, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
| | - Yukiko Yoshida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-Ku, Tokyo, 156-8506, Japan
| | - Yusuke Kasuga
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Takeshi Kondo
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Hiroaki Yaguchi
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Masanobu Suzuki
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Hiroki Ishida
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-Ku, Tokyo, 156-8506, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, Hokkaido, 060-8638, Japan.
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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Proteomic approaches for the profiling of ubiquitylation events and their applications in drug discovery. J Proteomics 2020; 231:103996. [PMID: 33017648 DOI: 10.1016/j.jprot.2020.103996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 09/27/2020] [Indexed: 01/23/2023]
Abstract
Protein ubiquitylation regulates almost all aspects of the biological processes including gene expression, DNA repair, cell proliferation and apoptosis in eukaryotic cells. Dysregulation of protein ubiquitylation caused by abnormal expression of enzymes in the ubiquitin system results in the onset of many diseases including cancer, neurodegenerative diseases, and metabolic syndromes. Therefore, targeting the ubiquitin system becomes a promising research area in drug discovery. Identification of protein ubiquitylation sites is critical for revealing the key ubiquitylation events associated with diseases and specific signaling pathways and for elucidating the biological functions of the specific ubiquitylation events. Many approaches that enrich for the ubiquitylated proteins and ubiquitylated peptides at the protein and peptide levels have been developed to facilitate their identification by MS. In this paper, we will review the proteomic approaches available for the identification of ubiquitylation events at the proteome scale and discuss their advantages and limitations. We will also brief the application of the profiling of ubiquitylation events in drug target discovery and in target validation for proteolysis-targeting chimera (PROTAC). Possible future research directions in this field will also be discussed. SIGNIFICANCE: Ubiquitylation plays critical roles in regulating many biological processes in eukaryotic cells. Identification of ubiquitylation sites can provide the essential information for the functional study of the specific modified substrates. Since ubiquitylated proteins have much lower abundance than non-ubiquitylated proteins, enrichment of ubiquitylated proteins or peptides is critical for their identification by MS. This review focuses on different enrichment approaches that facilitate their isolation and identification by MS and discusses the advantages and drawbacks of these approaches. The application of the profiling of ubiquitylation events in drug target discovery and future research directions will be beneficial to the research community.
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Kumar D, Ambasta RK, Kumar P. Ubiquitin biology in neurodegenerative disorders: From impairment to therapeutic strategies. Ageing Res Rev 2020; 61:101078. [PMID: 32407951 DOI: 10.1016/j.arr.2020.101078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
The abnormal accumulation of neurotoxic proteins is the typical hallmark of various age-related neurodegenerative disorders (NDDs), including Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis and Multiple sclerosis. The anomalous proteins, such as Aβ, Tau in Alzheimer's disease and α-synuclein in Parkinson's disease, perturb the neuronal physiology and cellular homeostasis in the brain thereby affecting the millions of human lives across the globe. Here, ubiquitin proteasome system (UPS) plays a decisive role in clearing the toxic metabolites in cells, where any aberrancy is widely reported to exaggerate the neurodegenerative pathologies. In spite of well-advancement in the ubiquitination research, their molecular markers and mechanisms for target-specific protein ubiquitination and clearance remained elusive. Therefore, this review substantiates the role of UPS in the brain signaling and neuronal physiology with their mechanistic role in the NDD's specific pathogenic protein clearance. Moreover, current and future promising therapies are discussed to target UPS-mediated neurodegeneration for better public health.
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47
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Leveraging nature's biomolecular designs in next-generation protein sequencing reagent development. Appl Microbiol Biotechnol 2020; 104:7261-7271. [PMID: 32617618 DOI: 10.1007/s00253-020-10745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 01/18/2023]
Abstract
Next-generation approaches for protein sequencing are now emerging that could have the potential to revolutionize the field in proteomics. One such sequencing method involves fluorescence-based imaging of immobilized peptides in which the N-terminal amino acid of a polypeptide is readout sequentially by a series of fluorescently labeled biomolecules. When selectively bound to a specific N-terminal amino acid, the NAAB (N-terminal amino acid binder) affinity reagent identifies the amino acid through its associated fluorescence tag. A key technical challenge in implementing this fluoro-sequencing approach is the need to develop NAAB affinity reagents with the high affinity and selectivity for specific N-terminal amino acids required for this biotechnology application. One approach to develop such a NAAB affinity reagent is to leverage naturally occurring biomolecules that bind amino acids and/or peptides. Here, we describe several candidate biomolecules that could be considered for this purpose and discuss the potential for developability of each. Key points • Next-generation sequencing methods are emerging that could revolutionize proteomics. • Sequential readout of N-terminal amino acids by fluorescent-tagged affinity reagents. • Native peptide/amino acid binders can be engineered into affinity reagents. • Protein size and structure contribute to feasibility of reagent developability.
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Liu X, Zhang X, Lv D, Yuan Y, Zheng G, Zhou D. Assays and technologies for developing proteolysis targeting chimera degraders. Future Med Chem 2020; 12:1155-1179. [PMID: 32431173 PMCID: PMC7333641 DOI: 10.4155/fmc-2020-0073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Targeted protein degradation by small-molecule degraders represents an emerging mode of action in drug discovery. Proteolysis targeting chimeras (PROTACs) are small molecules that can recruit an E3 ligase and a protein of interest (POI) into proximity, leading to induced ubiquitination and degradation of the POI by the proteasome system. To date, the design and optimization of PROTACs remain empirical due to the complicated mechanism of induced protein degradation. Nevertheless, it is increasingly appreciated that profiling step-by-step along the ubiquitin-proteasome degradation pathway using biochemical and biophysical assays are essential in understanding the structure-activity relationship and facilitating the rational design of PROTACs. This review aims to summarize these assays and to discuss the potential of expanding the toolbox with other new techniques.
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Affiliation(s)
- Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
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Zhao B, Tsai YC, Jin B, Wang B, Wang Y, Zhou H, Carpenter T, Weissman AM, Yin J. Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond. Pharmacol Rev 2020; 72:380-413. [PMID: 32107274 PMCID: PMC7047443 DOI: 10.1124/pr.118.015651] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell. SIGNIFICANCE STATEMENT: The post-translational modification of proteins with ubiquitin alters the fate and function of proteins in diverse ways. Protein engineering is fundamentally transforming research in this area, providing new mechanistic insights and allowing for the exploration of concepts that can potentially be applied to therapeutic intervention.
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Affiliation(s)
- Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yien Che Tsai
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bufan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yiyang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Han Zhou
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Tomaya Carpenter
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Allan M Weissman
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Jun Yin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
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50
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Liang YY, Zhang J, Cui H, Shao ZS, Cheng C, Wang YB, Wang HS. Fluorescence resonance energy transfer (FRET)-based nanoarchitecture for monitoring deubiquitinating enzyme activity. Chem Commun (Camb) 2020; 56:3183-3186. [PMID: 32067022 DOI: 10.1039/c9cc09808a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A novel nanoarchitecture (MSN-Tb-UbR) was prepared by modifying rhodamine B-labelled Ubs (Ub-Rs) on the surface of mesoporous silica nanoparticles (MSNs) loaded with Tb3+-complexes. The MSN-Tb-UbR exhibits ratiometric sensing ability for DUB (UCH-L1) with good sensitivity and selectivity.
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Affiliation(s)
- Yan-Yan Liang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, China.
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