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Akiyama M, Mizokami T, Miyamoto S, Ikeda Y. Kaempferol increases intracellular ATP content in C 2C 12 myotubes under hypoxic conditions by suppressing the HIF-1α stabilization and/or by enhancing the mitochondrial complex IV activity. J Nutr Biochem 2022; 103:108949. [PMID: 35122998 DOI: 10.1016/j.jnutbio.2022.108949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Kaempferol (KMP) has numerous important biological functions, and we recently showed that it remarkably increased intracellular adenosine triphosphate (ATP) content in C2C12 myotubes under hypoxic conditions. Since intracellular ATP is generated by aerobic energy metabolism or anaerobic glycolysis, hypoxia inducible factor-1α (HIF-1α) has been shown to be associated with metabolic remodeling and causes metabolic shift from aerobic energy metabolism to anaerobic glycolysis in response to hypoxic conditions. Here, we investigate the effects of KMP under hypoxic conditions on the stabilization of HIF-1α in C2C12 myotubes and its underlying molecular mechanisms. Constitutive HIF-1α protein expression was observed in C2C12 myotubes, and its expression under hypoxic conditions was remarkably suppressed by KMP by reducing its stability; thus, resulting in an increase in ATP content. Furthermore, KMP strikingly increased the ubiquitination of HIF-1α and promoted its degradation via the ubiquitin proteasome system. Inhibition of HIF-1α by KMP resulted in the abrogation of the expression of glycolytic enzymes such as lactate dehydrogenase A and pyruvate dehydrogenase kinase isozyme 1. In addition, the metabolome profiling showed that KMP promoted oxidative energy production, while the mitochondrial complex activity assay indicated that KMP increased the activity of mitochondrial complex IV. Finally, we showed that KMP inhibited HIF-1α expression and increased intracellular ATP content in the soleus muscle of rats. Taken together, these results suggest that KMP increases intracellular ATP content under hypoxic conditions by suppressing the HIF-1α stabilization and/or by enhancing the mitochondrial complex IV activity in muscle.
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Key Words
- 2-OG, 2-oxoglutaric acid
- 3-PG, 3-phosphoglyceric acid
- ADP, adenosine diphosphate
- ATP, adenosine triphosphate
- AcCoA, acetyl CoA
- C(2)C(12) myotube
- CE-TOFMS, capillary electrophoresis time-of-flight mass spectrometry
- CHX, cycloheximide
- DFO, deferoxamine mesylate
- DMEM, Dulbecco's modified Eagle medium
- DMSO, dimethylsulfoxide
- EGCG, epigallocatechin gallate
- F1,6P, fructose-1,6-bisphosphate
- F6P, fructose-6-phosphate
- FAD, flavin adenine dinucleotide
- FBS, fetal bovine serum
- G6P, glucose-6-phosphate
- GAP, glyceraldehyde-3-phosphate
- HIF, hypoxia inducible factor
- HIF-1α, hypoxia
- HRE, hypoxia response element
- HS, horse serum
- HSP, heat shock protein
- KMP, kaempferol
- LDHA, lactate dehydrogenase A
- Lac, lactacystin
- NAD, nicotinamide adenine dinucleotide
- PBS, phosphate-buffered saline
- PDH, pyruvate dehydrogenase
- PDK1, pyruvate dehydrogenase kinase isozyme 1
- PEP, phosphoenolpyruvic acid
- PHD, prolyl hydroxylase
- RACK, receptor for activated C kinase
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- TCA, tricarboxylic acid
- Ub, ubiquitin
- VHL, von Hippel–Lindau
- kaempferol
- metabolome profiling
- mitochondria
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Affiliation(s)
- Minoru Akiyama
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Tsubasa Mizokami
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Shingo Miyamoto
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Yasutaka Ikeda
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan.
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Upadhyay A. Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases. Acta Pharm Sin B 2021; 11:2995-3014. [PMID: 34729300 PMCID: PMC8546668 DOI: 10.1016/j.apsb.2021.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023] Open
Abstract
Cells have different sets of molecules for performing an array of physiological functions. Nucleic acids have stored and carried the information throughout evolution, whereas proteins have been attributed to performing most of the cellular functions. To perform these functions, proteins need to have a unique conformation and a definite lifespan. These attributes are achieved by a highly coordinated protein quality control (PQC) system comprising chaperones to fold the proteins in a proper three-dimensional structure, ubiquitin-proteasome system for selective degradation of proteins, and autophagy for bulk clearance of cell debris. Many kinds of stresses and perturbations may lead to the weakening of these protective cellular machinery, leading to the unfolding and aggregation of cellular proteins and the occurrence of numerous pathological conditions. However, modulating the expression and functional efficiency of molecular chaperones, E3 ubiquitin ligases, and autophagic proteins may diminish cellular proteotoxic load and mitigate various pathological effects. Natural medicine and small molecule-based therapies have been well-documented for their effectiveness in modulating these pathways and reestablishing the lost proteostasis inside the cells to combat disease conditions. The present article summarizes various similar reports and highlights the importance of the molecules obtained from natural sources in disease therapeutics.
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Key Words
- 17-AAG, 17-allylamino-geldanamycin
- APC, anaphase-promoting complex
- Ageing
- Autophagy
- BAG, BCL2-associated athanogene
- CAP, chaperone-assisted proteasomal degradation
- CASA, chaperone-assisted selective autophagy
- CHIP, carboxy-terminus of HSC70 interacting protein
- CMA, chaperone-mediated autophagy
- Cancer
- Chaperones
- DUBs, deubiquitinases
- Drug discovery
- EGCG, epigallocatechin-3-gallate
- ESCRT, endosomal sorting complexes required for transport
- HECT, homologous to the E6-AP carboxyl terminus
- HSC70, heat shock cognate 70
- HSF1, heat shock factor 1
- HSP, heat shock protein
- KFERQ, lysine-phenylalanine-glutamate-arginine-glutamine
- LAMP2a, lysosome-associated membrane protein 2a
- LC3, light chain 3
- NBR1, next to BRCA1 gene 1
- Natural molecules
- Neurodegeneration
- PQC, protein quality control
- Proteinopathies
- Proteostasis
- RING, really interesting new gene
- UPS, ubiquitin–proteasome system
- Ub, ubiquitin
- Ubiquitin proteasome system
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Bandar Sindari, Kishangarh, Ajmer, Rajasthan 305817, India
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Barata-Antunes C, Alves R, Talaia G, Casal M, Gerós H, Mans R, Paiva S. Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking. Comput Struct Biotechnol J 2021; 19:1713-37. [PMID: 33897977 DOI: 10.1016/j.csbj.2021.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g., nutrient fluctuations or different stresses). At the heart of this mechanism lies a network of proteins that includes the arrestin‐related trafficking adaptors (ARTs) which link the ubiquitin ligase Rsp5 to nutrient transporters and endocytic factors. Transporter conformational changes, as well as dynamic interactions between its cytosolic termini/loops and with lipids of the plasma membrane, are also critical during the endocytic process. Here, we review the current knowledge and recent findings on the molecular mechanisms involved in nutrient transporter endocytosis, both in the budding yeast Saccharomyces cerevisiae and in some species of the filamentous fungus Aspergillus. We elaborate on the physiological importance of tightly regulated endocytosis for cellular fitness under dynamic conditions found in nature and highlight how further understanding and engineering of this process is essential to maximize titer, rate and yield (TRY)-values of engineered cell factories in industrial biotechnological processes.
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Key Words
- AAs, amino acids
- ACT, amino Acid/Choline Transporter
- AP, adaptor protein
- APC, amino acid-polyamine-organocation
- Arg, arginine
- Arrestins
- Arts, arrestin‐related trafficking adaptors
- Asp, aspartic acid
- Aspergilli
- Biotechnology
- C, carbon
- C-terminus, carboxyl-terminus
- Cell factories
- Conformational changes
- Cu, copper
- DUBs, deubiquitinating enzymes
- EMCs, eisosome membrane compartments
- ER, endoplasmic reticulum
- ESCRT, endosomal sorting complex required for transport
- Endocytic signals
- Endocytosis
- Fe, iron
- Fungi
- GAAC, general amino acid control
- Glu, glutamic acid
- H+, proton
- IF, inward-facing
- LAT, L-type Amino acid Transporter
- LID, loop Interaction Domain
- Lys, lysine
- MCCs, membrane compartments containing the arginine permease Can1
- MCCs/eisosomes
- MCPs, membrane compartments of Pma1
- MFS, major facilitator superfamily
- MVB, multi vesicular bodies
- Met, methionine
- Metabolism
- Mn, manganese
- N, nitrogen
- N-terminus, amino-terminus
- NAT, nucleobase Ascorbate Transporter
- NCS1, nucleobase/Cation Symporter 1
- NCS2, nucleobase cation symporter family 2
- NH4+, ammonium
- Nutrient transporters
- OF, outward-facing
- PEST, proline (P), glutamic acid (E), serine (S), and threonine (T)
- PM, plasma membrane
- PVE, prevacuolar endosome
- Saccharomyces cerevisiae
- Signaling pathways
- Structure-function
- TGN, trans-Golgi network
- TMSs, transmembrane segments
- TORC1, target of rapamycin complex 1
- TRY, titer, rate and yield
- Trp, tryptophan
- Tyr, tyrosine
- Ub, ubiquitin
- Ubiquitylation
- VPS, vacuolar protein sorting
- W/V, weight per volume
- YAT, yeast Amino acid Transporter
- Zn, Zinc
- fAATs, fungal AA transporters
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Liu Y, Liu X, Zhang N, Yin M, Dong J, Zeng Q, Mao G, Song D, Liu L, Deng H. Berberine diminishes cancer cell PD-L1 expression and facilitates antitumor immunity via inhibiting the deubiquitination activity of CSN5. Acta Pharm Sin B 2020; 10:2299-2312. [PMID: 33354502 PMCID: PMC7745128 DOI: 10.1016/j.apsb.2020.06.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 12/28/2022] Open
Abstract
Programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) blocking therapy has become a major pillar of cancer immunotherapy. Compared with antibodies targeting, small-molecule checkpoint inhibitors which have favorable pharmacokinetics are urgently needed. Here we identified berberine (BBR), a proven anti-inflammation drug, as a negative regulator of PD-L1 from a set of traditional Chinese medicine (TCM) chemical monomers. BBR enhanced the sensitivity of tumour cells to co-cultured T-cells by decreasing the level of PD-L1 in cancer cells. In addition, BBR exerted its antitumor effect in Lewis tumor xenograft mice through enhancing tumor-infiltrating T-cell immunity and attenuating the activation of immunosuppressive myeloid-derived suppressor cells (MDSCs) and regulatory T-cells (Tregs). BBR triggered PD-L1 degradation through ubiquitin (Ub)/proteasome-dependent pathway. Remarkably, BBR selectively bound to the glutamic acid 76 of constitutive photomorphogenic-9 signalosome 5 (CSN5) and inhibited PD-1/PD-L1 axis through its deubiquitination activity, resulting in ubiquitination and degradation of PD-L1. Our data reveals a previously unrecognized antitumor mechanism of BBR, suggesting BBR is small-molecule immune checkpoint inhibitor for cancer treatment.
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Key Words
- AMC, 7-amino-4-methylcoumarin
- BBR, berberine
- Baf, bafilomycin
- Berberine
- CHX, cycloheximide
- COP9 signalosome 5
- CQ, chloroquine
- CSN5, COP9 signalosome 5
- IB, immunoblotting
- ICB, immune checkpoint blockade
- IFN-γ, interferon-gamma
- IHC, immunohistochemistry
- Immune checkpoint blockade
- MDSCs, myeloid-derived suppressor cells
- NFAT, nuclear factor of activated T-cells
- NSCLC, non-small cell lung cancer
- PD-1, programmed cell death-1
- PD-1/PD-L1 axis
- PD-L1
- PD-L1, programmed cell death ligand-1
- SPR, surface plasmon resonance
- T-cell immunity
- TCM, traditional Chinese medicine
- TILs, tumor-infiltrating lymphocytes
- TNF-α, tumor necrosis factor-α
- Tregs, regulatory T-lymphocytes
- Ub, ubiquitin
- qRT-PCR, quantitative real-time polymerase chain reaction
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Affiliation(s)
- Yang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaojia Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Na Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mingxiao Yin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jingwen Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qingxuan Zeng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Genxiang Mao
- Zhejiang Provincial Key Lab of Geriatrics, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310013, China
| | - Danqing Song
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Liu
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266034, China
- Corresponding author. Tel.: +86 10 63169876, fax: +86 10 63017302 (Hongbin Deng); Tel.: +86 532 68661375, fax: +86 532 68661111 (Lu Liu).
| | - Hongbin Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Corresponding author. Tel.: +86 10 63169876, fax: +86 10 63017302 (Hongbin Deng); Tel.: +86 532 68661375, fax: +86 532 68661111 (Lu Liu).
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Liu Z, Zhao T, Li Z, Sun K, Fu Y, Cheng T, Guo J, Yu B, Shi X, Liu H. Discovery of [1,2,3]triazolo[4,5- d]pyrimidine derivatives as highly potent, selective, and cellularly active USP28 inhibitors. Acta Pharm Sin B 2020; 10:1476-1491. [PMID: 32963944 PMCID: PMC7488365 DOI: 10.1016/j.apsb.2019.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/20/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin specific peptidase 28 (USP28) is closely associated to the occurrence and development of various malignancies, and thus has been validated as a promising therapeutic target for cancer therapy. To date, only few USP28 inhibitors with moderate inhibitory activity have been reported, highly potent and selective USP28 inhibitors with new chemotypes remain to be discovered for pathologically investigating the roles of deubiquitinase. In this current study, we reported the synthesis and biological evaluation of new [1,2,3]triazolo[4,5-d]pyrimidine derivatives as potent USP28 inhibitors. Especially, compound 19 potently inhibited USP28 (IC50 = 1.10 ± 0.02 μmol/L, Kd = 40 nmol/L), showing selectivity over USP7 and LSD1 (IC50 > 100 μmol/L). Compound 19 was cellularly engaged to USP28 in gastric cancer cells. Compound 19 reversibly bound to USP28 and directly affected its protein levels, thus inhibiting the proliferation, cell cycle at S phase, and epithelial-mesenchymal transition (EMT) progression in gastric cancer cell lines. Docking studies were performed to rationalize the potency of compound 19. Collectively, compound 19 could serve as a new tool compound for the development of new USP28 inhibitors for exploring the roles of deubiquitinase in cancers.
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Key Words
- BLI, biolayer interferometry technology
- CHX, cycloheximide
- DUBs, deubiquitinating enzymes
- Deubiquitination
- EMT, epithelial-mesenchymal transition
- EdU, 5-ethynyl-2′-deoxyuridine
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- Gastric cancer
- IC50, half maximal inhibitory concentration
- Kd, dissociation constant
- LSD1, lysine specific demethylase 1
- MG132, proteasome inhibitor
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2-5-diphenyltetrazoliumbromide
- NSCLC, non-small cell lung cancer
- Tris, 2-amino-2-(hydroxymethyl)-1,3-propanediol
- USP28 inhibitors
- USP28, ubiquitin specific peptidase 28
- USP7, ubiquitin specific peptidase 7
- Ub, ubiquitin
- Ub-AMC, ubiquitin-7-amido-4-methylcoumarin
- [1,2,3]Triazolo[4,5-d]pyrimidine derivatives
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Affiliation(s)
| | | | | | | | | | | | | | - Bin Yu
- Corresponding authors. Tel./fax: +86 371 67781908.
| | - Xiaojing Shi
- Corresponding authors. Tel./fax: +86 371 67781908.
| | - Hongmin Liu
- Corresponding authors. Tel./fax: +86 371 67781908.
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Kwon D, Kim SM, Correia MA. Cytochrome P450 endoplasmic reticulum-associated degradation (ERAD): therapeutic and pathophysiological implications. Acta Pharm Sin B 2020; 10:42-60. [PMID: 31993306 PMCID: PMC6976991 DOI: 10.1016/j.apsb.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
The hepatic endoplasmic reticulum (ER)-anchored cytochromes P450 (P450s) are mixed-function oxidases engaged in the biotransformation of physiologically relevant endobiotics as well as of myriad xenobiotics of therapeutic and environmental relevance. P450 ER-content and hence function is regulated by their coordinated hemoprotein syntheses and proteolytic turnover. Such P450 proteolytic turnover occurs through a process known as ER-associated degradation (ERAD) that involves ubiquitin-dependent proteasomal degradation (UPD) and/or autophagic-lysosomal degradation (ALD). Herein, on the basis of available literature reports and our own recent findings of in vitro as well as in vivo experimental studies, we discuss the therapeutic and pathophysiological implications of altered P450 ERAD and its plausible clinical relevance. We specifically (i) describe the P450 ERAD-machinery and how it may be repurposed for the generation of antigenic P450 peptides involved in P450 autoantibody pathogenesis in drug-induced acute hypersensitivity reactions and liver injury, or viral hepatitis; (ii) discuss the relevance of accelerated or disrupted P450-ERAD to the pharmacological and/or toxicological effects of clinically relevant P450 drug substrates; and (iii) detail the pathophysiological consequences of disrupted P450 ERAD, contributing to non-alcoholic fatty liver disease (NAFLD)/non-alcoholic steatohepatitis (NASH) under certain synergistic cellular conditions.
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Key Words
- 3MA, 3-methyladenine
- AAA, ATPases associated with various cellular activities
- ACC1, acetyl-CoA carboxylase 1
- ACC2, acetyl-CoA carboxylase 2
- ACHE, acetylcholinesterase
- ACOX1, acyl-CoA oxidase 1
- ALD, autophagic-lysosomal degradation
- AMPK1
- AP-1, activator protein 1
- ASK1, apoptosis signal-regulating kinase
- ATF2, activating transcription factor 2
- AdipoR1, gene of adiponectin receptor 1
- Atg14, autophagy-related 14
- CBZ, carbamazepine
- CHIP E3 ubiquitin ligase
- CHIP, carboxy-terminus of Hsc70-interacting protein
- Cytochromes P450
- Endoplasmic reticulum-associated degradation
- FOXO, forkhead box O
- Fas, fatty acid synthase
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- INH, isoniazid
- IRS1, insulin receptor substrate 1
- Il-1β, interleukin 1 β
- Il-6, interleukin 6
- Insig1, insulin-induced gene 1
- JNK1
- Lpl, lipoprotein lipase
- Mcp1, chemokine (C–C motif) ligand 1
- Non-alcoholic fatty liver disease
- Non-alcoholic steatohepatitis
- Pgc1, peroxisome proliferator-activated receptor coactivator 1
- SREBP1c, sterol regulatory element binding transcription factor 1c
- Scd1, stearoyl-coenzyme A desaturase
- Tnf, tumor necrosis factor
- UPD, ubiquitin (Ub)-dependent proteasomal degradation
- Ub, ubiquitin
- gp78/AMFR E3 ubiquitin ligase
- gp78/AMFR, autocrine motility factor receptor
- shRNAi, shRNA interference
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Milan E, Perini T, Resnati M, Orfanelli U, Oliva L, Raimondi A, Cascio P, Bachi A, Marcatti M, Ciceri F, Cenci S. A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells. Autophagy 2016; 11:1161-78. [PMID: 26043024 PMCID: PMC4590585 DOI: 10.1080/15548627.2015.1052928] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
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Key Words
- APC, allophycocyanin
- Ab, antibody
- BM, bone marrow
- Baf A1, bafilomycin A1
- Btz, bortezomib
- ER, endoplasmic reticulum
- ERGIC, ER-Golgi intermediate compartment
- GO, gene ontology
- HCQ, hydroxychloroquine
- IP, immunoprecipitation
- Ig, immunoglobulin
- LC-MS/MS, liquid chromatography–tandem mass spectrometry
- MM, multiple myeloma
- PBS, phosphate-buffered saline
- PC, plasma cell
- PI, proteasome inhibitor
- Rapa, rapamycin
- SILAC, stable isotope labeling in cell culture
- SQSTM1
- UPR, unfolded protein response
- UPS, ubiquitin-proteasome system
- Ub, ubiquitin
- aggregate
- amc, 7-amino-4-methylcoumarin
- autophagy
- bortezomib
- endoplasmic reticulum
- multiple myeloma
- p62
- pAb, polyclonal antibody
- plasma cells
- proteasome
- proteasome inhibitors
- proteostasis
- ubiquitin
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Affiliation(s)
- Enrico Milan
- a San Raffaele Scientific Institute; Division of Genetics and Cell Biology ; Milan , Italy
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Xu D, Zhang T, Xiao J, Zhu K, Wei R, Wu Z, Meng H, Li Y, Yuan J. Modification of BECN1 by ISG15 plays a crucial role in autophagy regulation by type I IFN/interferon. Autophagy 2016; 11:617-28. [PMID: 25906440 DOI: 10.1080/15548627.2015.1023982] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
ISG15 (ISG15 ubiquitin-like modifier), a ubiquitin-like protein, is one of the major type I IFN (interferon) effector systems. ISG15 can be conjugated to target proteins (ISGylation) via the stepwise action of E1, E2, and E3 enzymes. Conjugated ISG15 can be removed (deISGylated) from target proteins by USP18 (ubiquitin-specific peptidase 18). Here we investigated the role of deISGylation by USP18 in regulating autophagy and EGFR degradation in cells treated with type I IFNs. We show that type I IFN induced expression of ISG15 leads to ISGylation of BECN1 at Lys117, as well as Lys263, Lys265, and Lys266 which competes with Lys63 ubiquitination of BECN1. We demonstrate that ISGylation of BECN1 at Lys117, as well as Lys263, Lys265, and Lys266 serve an important role in negative regulation of intracellular processes including autophagy and EGFR degradation that are critically dependent upon the activity of class III PtdIns 3-kinase. Our studies provide fundamental new mechanistic insights into the innate immunity response implemented by type I IFNs.
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Key Words
- AKT/PKB, v-akt murine thymoma viral oncogene homolog
- ATG, autophagy-related
- BECN1
- BECN1, Beclin 1, autophagy-related
- EGF, epidermal growth factor
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HERC5, HECT, and RLD domain containing E3 ubiquitin protein ligase 5
- IFN, interferon
- ISG15
- ISG15, ISG15 ubiquitin-like modifier
- LC3, microtubule-associated protein 1 light chain 3
- MTOR, mechanistic target of rapamycin
- MX1, MX dynamin-like GTPase 1
- PIK3C3, phosphatidylinositol 3-kinase, catalytic subunit type 3
- RPS6KB, ribosomal protein S6 kinase, 70kDa, polypeptide
- SQSTM1/p62, sequestosome 1
- UBA7, ubiquitin-like modifier activating enzyme 7
- USP18
- USP18, ubiquitin specific peptidase 18
- Ub, ubiquitin
- autophagy
- type I IFN
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Affiliation(s)
- Daichao Xu
- a Interdisciplinary Research Center on Biology and Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences ; Shanghai , China
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Lancini C, Gargiulo G, van den Berk PCM, Citterio E. Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice. Data Brief 2016; 6:556-61. [PMID: 26909367 PMCID: PMC4731422 DOI: 10.1016/j.dib.2015.12.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 12/18/2015] [Indexed: 12/04/2022] Open
Abstract
The data described here provide genome-wide expression profiles of murine primitive hematopoietic stem and progenitor cells (LSK) and of B cell populations, obtained by high throughput sequencing. Cells are derived from wild-type mice and from mice deficient for the ubiquitin-specific protease 3 (USP3; Usp3Δ/Δ). Modification of histone proteins by ubiquitin plays a crucial role in the cellular response to DNA damage (DDR) (Jackson and Durocher, 2013) [1]. USP3 is a histone H2A deubiquitinating enzyme (DUB) that regulates ubiquitin-dependent DDR in response to DNA double-strand breaks (Nicassio et al., 2007; Doil et al., 2008) [2], [3]. Deletion of USP3 in mice increases the incidence of spontaneous tumors and affects hematopoiesis [4]. In particular, Usp3-knockout mice show progressive loss of B and T cells and decreased functional potential of hematopoietic stem cells (HSCs) during aging. USP3-deficient cells, including HSCs, display enhanced histone ubiquitination, accumulate spontaneous DNA damage and are hypersensitive to ionizing radiation (Lancini et al., 2014) [4]. To address whether USP3 loss leads to deregulation of specific molecular pathways relevant to HSC homeostasis and/or B cell development, we have employed the RNA-sequencing technology and investigated transcriptional differences between wild-type and Usp3Δ/Δ LSK, naïve B cells or in vitro activated B cells. The data relate to the research article “Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells” (Lancini et al., 2014) [4]. The RNA-sequencing and analysis data sets have been deposited in NCBI׳s Gene Expression Omnibus (Edgar et al., 2002) [5] and are accessible through GEO Series accession number GSE58495 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58495). With this article, we present validation of the RNA-seq data set through quantitative real-time PCR and comparative analysis.
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Affiliation(s)
- Cesare Lancini
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gaetano Gargiulo
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Paul C M van den Berk
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elisabetta Citterio
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Xu C, Feng K, Zhao X, Huang S, Cheng Y, Qian L, Wang Y, Sun H, Jin M, Chuang TH, Zhang Y. Regulation of autophagy by E3 ubiquitin ligase RNF216 through BECN1 ubiquitination. Autophagy 2015; 10:2239-50. [PMID: 25484083 PMCID: PMC4502788 DOI: 10.4161/15548627.2014.981792] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autophagy is an evolutionarily conserved biological process involved in an array of physiological and pathological events. Without proper control, autophagy contributes to various disorders, including cancer and autoimmune and inflammatory diseases. It is therefore of vital importance that autophagy is under careful balance. Thus, additional regulators undoubtedly deepen our understanding of the working network, and provide potential therapeutic targets for disorders. In this study, we found that RNF216 (ring finger protein 216), an E3 ubiquitin ligase, strongly inhibits autophagy in macrophages. Further exploration demonstrates that RNF216 interacts with BECN1, a key regulator in autophagy, and leads to ubiquitination of BECN1, thereby contributing to BECN1 degradation. RNF216 was involved in the ubiquitination of lysine 48 of BECN1 through direct interaction with the triad (2 RING fingers and a DRIL [double RING finger linked]) domain. We further showed that inhibition of autophagy through overexpression of RNF216 in alveolar macrophages promotes Listeria monocytogenes growth and distribution, while knockdown of RNF216 significantly inhibited these outcomes. These effects were confirmed in a mouse model of L. monocytogenes infection, suggesting that manipulating RNF216 expression could be a therapeutic approach. Thus, our study identifies a novel negative regulator of autophagy and suggests that RNF216 may be a target for treatment of inflammatory diseases.
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Key Words
- Atg, autophagy-related
- BALF, bronchoalveolar lavage fluid
- BECN1
- BMDM, bone marrow-derived macrophage
- CFU, colony-forming unit
- GFP, green fluorescent protein
- HRP, horseradish peroxidase
- LPS, lipopolysaccharide
- MAP1LC3A, microtubule-associated protein 1 light chain 3 α
- MOI, multiplicity of infection
- NFKB, nuclear factor of kappa light polypeptide gene enhancer in B-cells
- PBS, phosphate-buffered saline
- RIPK1, receptor (TNFRSF)-interacting serine-threonine kinase 1
- RNF216
- RNF216, ring finger protein 216;TIRAP, toll-interleukin 1 receptor (TIR) domain containing adaptor protein
- TICAM1/TRIF, toll-like receptor adaptor molecule 1
- TICAM2, toll-like receptor adaptor molecule 2
- TLR, toll-like receptor
- TNF, tumor necrosis factor
- TRAF, TNF receptor-associated factor
- Triad, 2 RING fingers and a DRIL (double RING finger linked)
- Ub, ubiquitin
- autophagy
- i.t., intratracheally
- protein degradation
- shRNA, short hairpin RNA
- ubiquitination
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Affiliation(s)
- Congfeng Xu
- a Shanghai Institute of Immunology; Institutes of Medical Sciences; Shanghai Jiao Tong University School of Medicine (SJTUSM); and Key Laboratory of Stem Cell Biology; Institute of Health Sciences; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences & SJTUSM ; Shanghai , China
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Xie Y, Kang R, Sun X, Zhong M, Huang J, Klionsky DJ, Tang D. Posttranslational modification of autophagy-related proteins in macroautophagy. Autophagy 2015; 11:28-45. [PMID: 25484070 DOI: 10.4161/15548627.2014.984267] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Macroautophagy is an intracellular catabolic process involved in the formation of multiple membrane structures ranging from phagophores to autophagosomes and autolysosomes. Dysfunction of macroautophagy is implicated in both physiological and pathological conditions. To date, 38 autophagy-related (ATG) genes have been identified as controlling these complicated membrane dynamics during macroautophagy in yeast; approximately half of these genes are clearly conserved up to human, and there are additional genes whose products function in autophagy in higher eukaryotes that are not found in yeast. The function of the ATG proteins, in particular their ability to interact with a number of macroautophagic regulators, is modulated by posttranslational modifications (PTMs) such as phosphorylation, glycosylation, ubiquitination, acetylation, lipidation, and proteolysis. In this review, we summarize our current knowledge of the role of ATG protein PTMs and their functional relevance in macroautophagy. Unraveling how these PTMs regulate ATG protein function during macroautophagy will not only reveal fundamental mechanistic insights into the regulatory process, but also provide new therapeutic targets for the treatment of autophagy-associated diseases.
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Affiliation(s)
- Yangchun Xie
- a Department of Oncology; Xiangya Hospital ; Central South University ; Changsha , Hunan , China
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Arrigoni A, Bertini L, De Gioia L, Papaleo E. Inhibitors of the Cdc34 acidic loop: A computational investigation integrating molecular dynamics, virtual screening and docking approaches. FEBS Open Bio 2014; 4:473-84. [PMID: 24918063 PMCID: PMC4050183 DOI: 10.1016/j.fob.2014.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 11/20/2022] Open
Abstract
Cdc34 is an E2 enzyme involved in protein ubiquitination and associated with some cancers. Cdc34 activity is modulated by phosphorylation-induced conformational changes of the acidic loop. We used computational approaches to identify potential inhibitory compounds for Cdc34. These inhibitors as molecular hinges stabilizing the acid loop in its inactive, closed conformation.
Among the different classes of enzymes involved in the ubiquitin pathway, E2 ubiquitin-conjugating enzymes occupy a central role in the ubiquitination cascade. Cdc34-like E2 enzymes are characterized by a 12–14 residue insertion in the proximity of the catalytic site, known as the acidic loop. Cdc34 ubiquitin-charging activity is regulated by CK2-dependent phosphorylation and the regulatory mechanism involves the acidic loop. Indeed, the phosphorylation stabilizes the loop in an open conformation that is competent for ubiquitin charging. Cdc34 is associated with a variety of diseases, such as hepatocellular carcinomas and prostatic adenocarcinomas. In light of its role, the discovery of potential inhibitory compounds would provide the mean to effectively modulate its activity. Here, we carried out a computational study based on molecular dynamics, virtual screening and docking to identify potential inhibitory compounds of Cdc34, modulating the acidic loop conformation. The molecules identified in this study have been designed to act as molecular hinges that can bind the acidic loop in its closed conformation, thus inhibiting the Cdc34-mediated ubiquitination cascade at the ubiquitin-charging step. In particular, we proposed a pharmacophore model featuring two amino groups in the central part of the model and two lateral aromatic chains, which respectively establish electrostatic interactions with the acidic loop (Asp 108 and Glu 109) and a hydrogen bond with Ser 139, which is one of the key residues for Cdc34 activity.
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Affiliation(s)
- Alberto Arrigoni
- Corresponding authors. Current address: Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark (E. Papaleo).
| | | | | | - Elena Papaleo
- Corresponding authors. Current address: Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark (E. Papaleo).
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Zaman MMU, Shinagawa T, Ishii S. Trim27-deficient mice are susceptible to streptozotocin-induced diabetes. FEBS Open Bio 2013; 4:60-4. [PMID: 24392305 PMCID: PMC3879403 DOI: 10.1016/j.fob.2013.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 11/29/2013] [Accepted: 12/16/2013] [Indexed: 01/17/2023] Open
Abstract
Tumor necrosis factor α (TNF-α) plays an important role in cell proliferation and apoptosis, and defects in TNF-α-induced apoptosis are associated with various diseases. TRIM27 is a tripartite motif (TRIM) protein containing RING finger, B-box, and coiled-coil domains. We recently reported that TRIM27 positively regulates TNF-α-induced apoptosis through deubiquitination of receptor-interacting protein 1 (RIP1). Multiple studies have suggested a link between TNF-α pathway and various diseases, such as diabetes and colitis. Here, we report that Trim27-deficient mice were susceptible to streptozotocin (STZ)-induced diabetes, a mouse model of diabetes. Infiltration of T cells and cleaved caspase-3 signals were enhanced, and β-cell mass was decreased in Trim27-deficient islets compared to wild-type islets. On the other hand, Trim27-mutation did not affect the dextran sodium sulphate (DSS)-induced colitis. These data support the idea that the TRIM27 mutation is responsible for the development of certain types of diseases. Trim27-deficient mice are susceptible to streptozotocin-induced diabetes. Infiltration of T cells is enhanced in Trim27-deficient islets. Beta-cell mass was decreased in Trim27-deficient islets. Trim27-deficient mice are not susceptible to dextran sodium sulphate-induced colitis.
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Affiliation(s)
- Mohammad Mahabub-Uz Zaman
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Toshie Shinagawa
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shunsuke Ishii
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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