1
|
Chueh KS, Lu JH, Juan TJ, Chuang SM, Juan YS. The Molecular Mechanism and Therapeutic Application of Autophagy for Urological Disease. Int J Mol Sci 2023; 24:14887. [PMID: 37834333 PMCID: PMC10573233 DOI: 10.3390/ijms241914887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Autophagy is a lysosomal degradation process known as autophagic flux, involving the engulfment of damaged proteins and organelles by double-membrane autophagosomes. It comprises microautophagy, chaperone-mediated autophagy (CMA), and macroautophagy. Macroautophagy consists of three stages: induction, autophagosome formation, and autolysosome formation. Atg8-family proteins are valuable for tracking autophagic structures and have been widely utilized for monitoring autophagy. The conversion of LC3 to its lipidated form, LC3-II, served as an indicator of autophagy. Autophagy is implicated in human pathophysiology, such as neurodegeneration, cancer, and immune disorders. Moreover, autophagy impacts urological diseases, such as interstitial cystitis /bladder pain syndrome (IC/BPS), ketamine-induced ulcerative cystitis (KIC), chemotherapy-induced cystitis (CIC), radiation cystitis (RC), erectile dysfunction (ED), bladder outlet obstruction (BOO), prostate cancer, bladder cancer, renal cancer, testicular cancer, and penile cancer. Autophagy plays a dual role in the management of urologic diseases, and the identification of potential biomarkers associated with autophagy is a crucial step towards a deeper understanding of its role in these diseases. Methods for monitoring autophagy include TEM, Western blot, immunofluorescence, flow cytometry, and genetic tools. Autophagosome and autolysosome structures are discerned via TEM. Western blot, immunofluorescence, northern blot, and RT-PCR assess protein/mRNA levels. Luciferase assay tracks flux; GFP-LC3 transgenic mice aid study. Knockdown methods (miRNA and RNAi) offer insights. This article extensively examines autophagy's molecular mechanism, pharmacological regulation, and therapeutic application involvement in urological diseases.
Collapse
Affiliation(s)
- Kuang-Shun Chueh
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, San-min District, Kaohsiung 80708, Taiwan;
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jian-He Lu
- Center for Agricultural, Forestry, Fishery, Livestock and Aquaculture Carbon Emission Inventory and Emerging Compounds (CAFEC), General Research Service Center, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Tai-Jui Juan
- Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
- Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Shu-Mien Chuang
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Yung-Shun Juan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, San-min District, Kaohsiung 80708, Taiwan;
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
| |
Collapse
|
2
|
Zhang X, Yang Z, Pan T, Long X, Sun Q, Wang PH, Li X, Kuang E. SARS-CoV-2 ORF3a induces RETREG1/FAM134B-dependent reticulophagy and triggers sequential ER stress and inflammatory responses during SARS-CoV-2 infection. Autophagy 2022; 18:2576-2592. [PMID: 35239449 PMCID: PMC9629087 DOI: 10.1080/15548627.2022.2039992] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 infections have resulted in a very large number of severe cases of COVID-19 and deaths worldwide. However, knowledge of SARS-CoV-2 infection, pathogenesis and therapy remains limited, emphasizing the urgent need for fundamental studies and drug development. Studies have shown that induction of macroautophagy/autophagy and hijacking of the autophagic machinery are essential for the infection and replication of SARS-CoV-2; however, the mechanism of this manipulation and the function of autophagy during SARS-CoV-2 infection remain unclear. In the present study, we identified ORF3a as an inducer of autophagy (in particular reticulophagy) and revealed that ORF3a localizes to the ER and induces RETREG1/FAM134B-related reticulophagy through the HMGB1-BECN1 (beclin 1) pathway. As a consequence, ORF3a induces ER stress and inflammatory responses through reticulophagy and then sensitizes cells to the acquisition of an ER stress-related early apoptotic phenotype and facilitates SARS-CoV-2 infection, suggesting that SARS-CoV-2 ORF3a hijacks reticulophagy and then disrupts ER homeostasis to induce ER stress and inflammatory responses during SARS-CoV-2 infection. These findings reveal the sequential induction of reticulophagy, ER stress and acute inflammatory responses during SARS-CoV-2 infection and imply the therapeutic potential of reticulophagy and ER stress-related drugs for COVID-19.Abbreviations: CQ: chloroquine; DEGs: differentially expressed genes; ER: endoplasmic reticulum; GSEA: gene set enrichment analysis; HMGB1: high mobility group box 1; HMOX1: heme oxygenase 1; MERS-CoV: Middle East respiratory syndrome coronavirus; RETREG1/FAM134B: reticulophagy regulator 1; RTN4: reticulon 4; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TN: tunicamycin.
Collapse
Affiliation(s)
- Xiaolin Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, China,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Ziwei Yang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, China,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Ting Pan
- Center for Infection and Immunity Studies, School of Medicine, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Xubing Long
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, China,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Qinqin Sun
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, China,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Pei-Hui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Shandong, Jinan, China
| | - Xiaojuan Li
- College of Clinic Medicine, Hubei University of Chinese Medicine, Hubei, Wuhan, China,CONTACT Xiaojuan Li College of Clinic Medicine, Hubei University of Chinese Medicine, Hubei, Wuhan430061, China
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, China,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China,Ersheng Kuang Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, Guangzhou, 510080, China
| |
Collapse
|
3
|
Agrotis A, Ketteler R. On ATG4B as Drug Target for Treatment of Solid Tumours-The Knowns and the Unknowns. Cells 2019; 9:cells9010053. [PMID: 31878323 PMCID: PMC7016753 DOI: 10.3390/cells9010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Autophagy is an evolutionary conserved stress survival pathway that has been shown to play an important role in the initiation, progression, and metastasis of multiple cancers; however, little progress has been made to date in translation of basic research to clinical application. This is partially due to an incomplete understanding of the role of autophagy in the different stages of cancer, and also to an incomplete assessment of potential drug targets in the autophagy pathway. While drug discovery efforts are on-going to target enzymes involved in the initiation phase of the autophagosome, e.g., unc51-like autophagy activating kinase (ULK)1/2, vacuolar protein sorting 34 (Vps34), and autophagy-related (ATG)7, we propose that the cysteine protease ATG4B is a bona fide drug target for the development of anti-cancer treatments. In this review, we highlight some of the recent advances in our understanding of the role of ATG4B in autophagy and its relevance to cancer, and perform a critical evaluation of ATG4B as a druggable cancer target.
Collapse
|
4
|
Agrotis A, von Chamier L, Oliver H, Kiso K, Singh T, Ketteler R. Human ATG4 autophagy proteases counteract attachment of ubiquitin-like LC3/GABARAP proteins to other cellular proteins. J Biol Chem 2019; 294:12610-12621. [PMID: 31315929 PMCID: PMC6709618 DOI: 10.1074/jbc.ac119.009977] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 01/01/2023] Open
Abstract
Microtubule-associated protein 1 light chain 3 α (LC3)/GABA type A receptor-associated protein (GABARAP) comprises a family of ubiquitin-like proteins involved in (macro)autophagy, an important intracellular degradation pathway that delivers cytoplasmic material to lysosomes via double-membrane vesicles called autophagosomes. The only currently known cellular molecules covalently modified by LC3/GABARAP are membrane phospholipids such as phosphatidylethanolamine in the autophagosome membrane. Autophagy-related 4 cysteine peptidase (ATG4) proteases process inactive pro-LC3/GABARAP before lipidation, and the same proteases can also deconjugate LC3/GABARAP from lipids. To determine whether LC3/GABARAP has other molecular targets, here we generated a pre-processed LC3B mutant (Q116P) that is resistant to ATG4-mediated deconjugation. Upon expression in human cells and when assessed by immunoblotting under reducing and denaturing conditions, deconjugation-resistant LC3B accumulated in multiple forms and at much higher molecular weights than free LC3B. We observed a similar accumulation when pre-processed versions of all mammalian LC3/GABARAP isoforms were expressed in ATG4-deficient cell lines, suggesting that LC3/GABARAP can attach also to other larger molecules. We identified ATG3, the E2-like enzyme involved in LC3/GABARAP lipidation, as one target of conjugation with multiple copies of LC3/GABARAP. We show that LC3B-ATG3 conjugates are distinct from the LC3B-ATG3 thioester intermediate formed before lipidation, and we biochemically demonstrate that ATG4B can cleave LC3B-ATG3 conjugates. Finally, we determined ATG3 residue Lys-243 as an LC3B modification site. Overall, we provide the first cellular evidence that mammalian LC3/GABARAP post-translationally modifies proteins akin to ubiquitination ("LC3ylation"), with ATG4 proteases acting like deubiquitinating enzymes to counteract this modification ("deLC3ylation").
Collapse
Affiliation(s)
- Alexander Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Lucas von Chamier
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Harriet Oliver
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Koshiro Kiso
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Tanya Singh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
5
|
Pengo N, Prak K, Costa JR, Luft C, Agrotis A, Freeman J, Gewinner CA, Chan AWE, Selwood DL, Kriston-Vizi J, Ketteler R. Identification of Kinases and Phosphatases That Regulate ATG4B Activity by siRNA and Small Molecule Screening in Cells. Front Cell Dev Biol 2018; 6:148. [PMID: 30443548 PMCID: PMC6221980 DOI: 10.3389/fcell.2018.00148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Autophagy protease ATG4B is a key regulator of the LC3/GABARAP conjugation system required for autophagosome formation, maturation and closure. Members of the ATG4 and the LC3/GABARAP family have been implicated in various diseases including cancer, and targeting the ATG4B protease has been suggested as a potential therapeutic anti-cancer strategy. Recently, it has been demonstrated that ATG4B is regulated by multiple post-translational modifications, including phosphorylation and de-phosphorylation. In order to identify regulators of ATG4B activity, we optimized a cell-based luciferase assay based on ATG4B-dependent release of Gaussia luciferase. We applied this assay in a proof-of-concept small molecule compound screen and identified activating compounds that increase cellular ATG4B activity. Next, we performed a high-throughput screen to identify kinases and phosphatases that regulate cellular ATG4B activity using siRNA mediated knockdown and cDNA overexpression. Of these, we provide preliminary evidence that the kinase AKT2 enhances ATG4B activity in cells. We provide all raw and processed data from the screens as a resource for further analysis. Overall, our findings provide novel insights into the regulation of ATG4B and highlight the importance of post-translational modifications of ATG4B.
Collapse
Affiliation(s)
- Niccolo Pengo
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Krisna Prak
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Joana R. Costa
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Christin Luft
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Alexander Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jamie Freeman
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - A. W. Edith Chan
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - David L. Selwood
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Janos Kriston-Vizi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| |
Collapse
|
6
|
Jo YK, Park NY, Park SJ, Kim BG, Shin JH, Jo DS, Bae DJ, Suh YA, Chang JH, Lee EK, Kim SY, Kim JC, Cho DH. O-GlcNAcylation of ATG4B positively regulates autophagy by increasing its hydroxylase activity. Oncotarget 2018; 7:57186-57196. [PMID: 27527864 PMCID: PMC5302982 DOI: 10.18632/oncotarget.11083] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022] Open
Abstract
Autophagy is a catabolic degradation process and maintains cellular homeostasis. And autophagy is activated in response to various stress conditions. Although O-GlcNAcylation functions a sensor for nutrient and stress, the relationship between O-GlcNAcylation and autophagy is largely unknown. Here, we identified that ATG4B is novel target for O-GlcNAcylation under metabolic stress condition. Treatment with PugNAc, an O-GlcNAcase inhibitor increased activation of autophagy in SH-SY5Y cells. Both bimolecular fluorescence complementation and immunoprecipitation assay indicated that OGT directly interacts with ATG4B in SH-SY5Y cells. We also found that the O-GlcNAcylated ATG4B was increased in autophagy activation conditions, and down-regulation of OGT reduces O-GlcNAcylation of ATG4B under low glucose condition. Furthermore, the proteolytic activity of ATG4B for LC3 cleavage was enhanced in PugNAc-treated cells. Taken together, these results imply that O-GlcNAcylation of ATG4B regulates autophagy activation by increasing its proteolytic activity under metabolic stress condition.
Collapse
Affiliation(s)
- Yoon Kyung Jo
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Na Yeon Park
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - So Jung Park
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Byung-Gyu Kim
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Ji Hyun Shin
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Doo Sin Jo
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Dong-Jun Bae
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Young-Ah Suh
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul, South Korea
| | - Sang-Yeob Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Jin Cheon Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.,Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Dong-Hyung Cho
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
7
|
Autophagy gene expression profiling identifies a defective microtubule-associated protein light chain 3A mutant in cancer. Oncotarget 2018; 7:41203-41216. [PMID: 27256984 PMCID: PMC5173052 DOI: 10.18632/oncotarget.9754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/23/2016] [Indexed: 12/01/2022] Open
Abstract
The cellular stress response autophagy has been implicated in various diseases including neuro-degeneration and cancer. The role of autophagy in cancer is not clearly understood and both tumour promoting and tumour suppressive effects of autophagy have been reported, which complicates the design of therapeutic strategies based on targeting the autophagy pathway. Here, we have systematically analyzed gene expression data for 47 autophagy genes for deletions, amplifications and mutations in various cancers. We found that several cancer types have frequent autophagy gene amplifications, whereas deletions are more frequent in prostate adenocarcinomas. Other cancer types such as glioblastoma and thyroid carcinoma show very few alterations in any of the 47 autophagy genes. Overall, individual autophagy core genes are altered at low frequency in cancer, suggesting that cancer cells require functional autophagy. Some autophagy genes show frequent single base mutations, such as members of the ULK family of protein kinases. Furthermore, we found hotspot mutations in the arginine-rich stretch in MAP1LC3A resulting in reduced cleavage of MAP1LC3A by ATG4B both in vitro and in vivo, suggesting a functional implication of this gene mutation in cancer development.
Collapse
|
8
|
Chorba JS, Galvan AM, Shokat KM. Stepwise processing analyses of the single-turnover PCSK9 protease reveal its substrate sequence specificity and link clinical genotype to lipid phenotype. J Biol Chem 2017; 293:1875-1886. [PMID: 29259136 DOI: 10.1074/jbc.ra117.000754] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/10/2017] [Indexed: 01/07/2023] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) down-regulates the low-density lipoprotein (LDL) receptor, elevating LDL cholesterol and accelerating atherosclerotic heart disease, making it a promising cardiovascular drug target. To achieve its maximal effect on the LDL receptor, PCSK9 requires autoproteolysis. After cleavage, PCSK9 retains its prodomain in the active site as a self-inhibitor. Unlike other proprotein convertases, however, this retention is permanent, inhibiting any further protease activity for the remainder of its life cycle. Such inhibition has proven a major challenge toward a complete biochemical characterization of PCSK9's proteolytic function, which could inform therapeutic approaches against its hypercholesterolemic effects. To address this challenge, we employed a cell-based, high-throughput method using a luciferase readout to evaluate the single-turnover PCSK9 proteolytic event. We combined this method with saturation mutagenesis libraries to interrogate the sequence specificities of PCSK9 cleavage and proteolysis-independent secretion. Our results highlight several key differences in sequence identity between these two steps, complement known structural data, and suggest that PCSK9 self-proteolysis is the rate-limiting step of secretion. Additionally, we found that for missense SNPs within PCSK9, alterations in both proteolysis and secretion are common. Last, we show that some SNPs allosterically modulate PCSK9's substrate sequence specificity. Our findings indicate that PCSK9 proteolysis acts as a commonly perturbed but critical switch in controlling lipid homeostasis and provide a new hope for the development of small-molecule PCSK9 inhibitors.
Collapse
Affiliation(s)
- John S Chorba
- From the Division of Cardiology, Department of Medicine, Zuckerberg San Francisco General and University of California, San Francisco, California 94110 and .,the Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94143
| | - Adri M Galvan
- the Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94143
| | - Kevan M Shokat
- the Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94143
| |
Collapse
|
9
|
Zhang Y, Ke X, Zheng C, Liu Y, Xie L, Zheng Z, Wang H. Development of a luciferase-based biosensor to assess enterovirus 71 3C protease activity in living cells. Sci Rep 2017; 7:10385. [PMID: 28871120 PMCID: PMC5583365 DOI: 10.1038/s41598-017-10840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/15/2017] [Indexed: 11/23/2022] Open
Abstract
Enterovirus 71 (EV71) is a major pathogen of hand, foot, and mouth disease (HFMD). To date, no antiviral drug has been approved to treat EV71 infection. Due to the essential role that EV71 3 C protease (3Cpro) plays in the viral life cycle, it is generally considered as a highly appealing target for antiviral drug development. In this study, we present a transgene-encoded biosensor that can accurately, sensitively and quantitatively report the proteolytic activity of EV71 3Cpro. This biosensor is based on the catalyzed activity of a pro-interleukin (IL)-1β-enterovirus 3Cpro cleavage site-Gaussia Luciferase (GLuc) fusion protein that we named i-3CS-GLuc. GLuc enzyme is inactive in the fusion protein because of aggregation caused by pro-IL-1β. However, the 3Cpro of EV71 and other enteroviruses, such as coxsackievirus A9 (CVA9), coxsackievirus B3 (CVB3), and poliovirus can recognize and process the canonical enterovirus 3Cpro cleavage site between pro-IL-1β and GLuc, thereby releasing and activating GLuc and resulting in increased luciferase activity. The high sensitivity, ease of use, and applicability as a transgene in cell-based assays of i-3CS-GLuc biosensor make it a powerful tool for studying viral protease proteolytic events in living cells and for achieving high-throughput screening of antiviral agents.
Collapse
Affiliation(s)
- Yuan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xianliang Ke
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, 510623, China
| | - Caishang Zheng
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, 510623, China
| | - Yan Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Li Xie
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhenhua Zheng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hanzhong Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
10
|
Pengo N, Agrotis A, Prak K, Jones J, Ketteler R. A reversible phospho-switch mediated by ULK1 regulates the activity of autophagy protease ATG4B. Nat Commun 2017; 8:294. [PMID: 28821708 PMCID: PMC5562857 DOI: 10.1038/s41467-017-00303-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 06/20/2017] [Indexed: 12/26/2022] Open
Abstract
Upon induction of autophagy, the ubiquitin-like protein LC3 is conjugated to phosphatidylethanolamine (PE) on the inner and outer membrane of autophagosomes to allow cargo selection and autophagosome formation. LC3 undergoes two processing steps, the proteolytic cleavage of pro-LC3 and the de-lipidation of LC3-PE from autophagosomes, both executed by the same cysteine protease ATG4. How ATG4 activity is regulated to co-ordinate these events is currently unknown. Here we find that ULK1, a protein kinase activated at the autophagosome formation site, phosphorylates human ATG4B on serine 316. Phosphorylation at this residue results in inhibition of its catalytic activity in vitro and in vivo. On the other hand, phosphatase PP2A-PP2R3B can remove this inhibitory phosphorylation. We propose that the opposing activities of ULK1-mediated phosphorylation and PP2A-mediated dephosphorylation provide a phospho-switch that regulates the cellular activity of ATG4B to control LC3 processing.Upon autophagy induction, LC3 is cleaved by the protease ATG4 and conjugated to the autophagosomal membrane; however, its removal is mediated by the same protease. Here the authors show that ULK1-mediated phosphorylation and PP2A-mediated dephosphorylation of ATG4 regulates its cellular activity to control LC3 processing.
Collapse
Affiliation(s)
- N Pengo
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - A Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - K Prak
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - J Jones
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - R Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
11
|
Skytte Rasmussen M, Mouilleron S, Kumar Shrestha B, Wirth M, Lee R, Bowitz Larsen K, Abudu Princely Y, O'Reilly N, Sjøttem E, Tooze SA, Lamark T, Johansen T. ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Autophagy 2017; 13:834-853. [DOI: https:/doi.org/10.1080/15548627.2017.1287651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 12/19/2023] Open
Affiliation(s)
- Mads Skytte Rasmussen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | | | - Birendra Kumar Shrestha
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Martina Wirth
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca Lee
- Structural Biology, The Francis Crick Institute, London, UK
| | - Kenneth Bowitz Larsen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Yakubu Abudu Princely
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nicola O'Reilly
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Eva Sjøttem
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
12
|
Skytte Rasmussen M, Mouilleron S, Kumar Shrestha B, Wirth M, Lee R, Bowitz Larsen K, Abudu Princely Y, O'Reilly N, Sjøttem E, Tooze SA, Lamark T, Johansen T. ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Autophagy 2017; 13:834-853. [PMID: 28287329 PMCID: PMC5446077 DOI: 10.1080/15548627.2017.1287651] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 12/29/2022] Open
Abstract
The cysteine protease ATG4B cleaves off one or more C-terminal residues of the inactive proform of proteins of the ortholog and paralog LC3 and GABARAP subfamilies of yeast Atg8 to expose a C-terminal glycine that is conjugated to phosphatidylethanolamine during autophagosome formation. We show that ATG4B contains a C-terminal LC3-interacting region (LIR) motif important for efficient binding to and cleavage of LC3 and GABARAP proteins. We solved the crystal structures of the GABARAPL1-ATG4B C-terminal LIR complex. Analyses of the structures and in vitro binding assays, using specific point mutants, clearly showed that the ATG4B LIR binds via electrostatic-, aromatic HP1 and hydrophobic HP2 pocket interactions. Both these interactions and the catalytic site-substrate interaction contribute to binding between LC3s or GABARAPs and ATG4B. We also reveal an unexpected role for ATG4B in stabilizing the unlipidated forms of GABARAP and GABARAPL1. In mouse embryonic fibroblast (MEF) atg4b knockout cells, GABARAP and GABARAPL1 were unstable and degraded by the proteasome. Strikingly, the LIR motif of ATG4B was required for stabilization of the unlipidated forms of GABARAP and GABARAPL1 in cells.
Collapse
Affiliation(s)
- Mads Skytte Rasmussen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | | | - Birendra Kumar Shrestha
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Martina Wirth
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca Lee
- Structural Biology, The Francis Crick Institute, London, UK
| | - Kenneth Bowitz Larsen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Yakubu Abudu Princely
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nicola O'Reilly
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Eva Sjøttem
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
13
|
Ugolino J, Ji YJ, Conchina K, Chu J, Nirujogi RS, Pandey A, Brady NR, Hamacher-Brady A, Wang J. Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling. PLoS Genet 2016; 12:e1006443. [PMID: 27875531 PMCID: PMC5119725 DOI: 10.1371/journal.pgen.1006443] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/21/2016] [Indexed: 12/13/2022] Open
Abstract
The most common cause of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal dementia is a hexanucleotide repeat expansion in C9orf72. Here we report a study of the C9orf72 protein by examining the consequences of loss of C9orf72 functions. Deletion of one or both alleles of the C9orf72 gene in mice causes age-dependent lethality phenotypes. We demonstrate that C9orf72 regulates nutrient sensing as the loss of C9orf72 decreases phosphorylation of the mTOR substrate S6K1. The transcription factor EB (TFEB), a master regulator of lysosomal and autophagy genes, which is negatively regulated by mTOR, is substantially up-regulated in C9orf72 loss-of-function animal and cellular models. Consistent with reduced mTOR activity and increased TFEB levels, loss of C9orf72 enhances autophagic flux, suggesting that C9orf72 is a negative regulator of autophagy. We identified a protein complex consisting of C9orf72 and SMCR8, both of which are homologous to DENN-like proteins. The depletion of C9orf72 or SMCR8 leads to significant down-regulation of each other’s protein level. Loss of SMCR8 alters mTOR signaling and autophagy. These results demonstrate that the C9orf72-SMCR8 protein complex functions in the regulation of metabolism and provide evidence that loss of C9orf72 function may contribute to the pathogenesis of relevant diseases. C9orf72 is one of many uncharacterized genes in the human genome. The presence of repeated nucleotides in the non-coding region of the C9orf72 gene (GGGGCC) has been linked to the neurodegenerative diseases Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). However, how the presence of these repeats in the gene leads to neurodegeneration is unknown. One possible explanation is that the repeats lead to a reduced expression of the C9orf72 gene and loss of function of the C9orf72 protein. Although C9orf72 is well-conserved among multi-cellular organisms, its protein function remains to be determined. In this study, we demonstrated that loss of C9orf72 reduces mTOR signaling and enhances autophagy. mTOR signaling and autophagy are important for the cellular maintenance of metabolic balances, especially under stress conditions. C9orf72 protein exists in a complex with another DENN-like protein, SMCR8, which also regulates mTOR signaling and autophagy. We generated mice lacking C9orf72, which died prematurely and showed dramatic upregulation of TFEB, a crucial transcriptional regulator of autophagy and lysosomal genes, that integrates mTOR activity state and autophagic capacity. We propose that C9orf72 function is important for metabolic control and its deficiency can contribute to the development of neurodegenerative diseases.
Collapse
Affiliation(s)
- Janet Ugolino
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yon Ju Ji
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Karen Conchina
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Justin Chu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Nathan R. Brady
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Maryland, United States of America
| | - Anne Hamacher-Brady
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Maryland, United States of America
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
14
|
Kulkarni GS, Zang W, Zhong Z. Nanoelectronic Heterodyne Sensor: A New Electronic Sensing Paradigm. Acc Chem Res 2016; 49:2578-2586. [PMID: 27668314 DOI: 10.1021/acs.accounts.6b00329] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoelectronic devices based on nanomaterials such as nanowires, carbon nanotubes, graphene, and other 2D nanomaterials offer extremely large surface-to-volume ratios, high carrier mobility, low power consumption, and high compatibility for integration with modern electronic technologies. These distinct advantages promise great potential for nanoelectronic devices as next generation chemical and biological sensors. Currently, majority of existing nanoelectronic sensors are direct current (DC) sensors, which rely ubiquitously on detection of conductance change associated with molecular adsorption. However, despite the simplicity of the conventional DC sensing technology, it also has severe limitations such as the Debye screening effect in ionic solutions, and the speed-sensitivity trade-off for the detection of charge-neutral molecules. Hence, the development of nanoelectronic sensors calls for new sensing platform technologies that can truly showcase the advantages of electronic sensors. In this Account, we will summarize recent efforts from our group on the development of a new electronic sensing paradigm, the nanoelectronic heterodyne sensors. Unlike conventional charge-detection based sensors, the heterodyne sensor explores the frequency mixing response between molecular dipoles and a nanoscale transistor. As an example, we first discuss the capability of heterodyne sensing in gas sensing applications by using graphene devices. Rapid (down to 0.1 s) and sensitive (down to 1 ppb) detection of a wide range of vapor analytes is achieved, representing orders of magnitude improvement over state-of-the-art nanoelectronic sensors. Furthermore, the heterodyne sensing technique enables electrical probing and tuning of the noncovalent physisorption of polar molecules on graphene surface for the first time. These results provide insight into small molecule-nanomaterial interaction dynamics and signify the ability to electrically tailor interactions, which can lead to rational designs of complex chemical processes for catalysis and drug discovery. Finally, we discuss the application of heterodyne sensing in solution for chemical and biological sensors by using carbon nanotube devices. The fundamental ionic screening effect can be mitigated by operating carbon nanotube field effect transistor as a heterodyne biosensor. Electrical detection of streptavidin binding to biotin in 100 mM buffer solution can be achieved at a frequency beyond 1 MHz. The results should promise a new biosensing platform for point-of-care detection, where biosensors functioning directly in physiologically relevant condition are desired.
Collapse
Affiliation(s)
- Girish S. Kulkarni
- Department
of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Ave, Ann Arbor, Michigan 48109, United States
- Arborsense, Inc., 1600 Huron Pkwy,
Bldg. 520, Ann Arbor, Michigan 48109, United States
| | - Wenzhe Zang
- Department
of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Ave, Ann Arbor, Michigan 48109, United States
| | - Zhaohui Zhong
- Department
of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Ave, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
15
|
Ribose 5-phosphate isomerase inhibits LC3 processing and basal autophagy. Cell Signal 2016; 28:1380-1388. [PMID: 27328773 PMCID: PMC4973805 DOI: 10.1016/j.cellsig.2016.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/17/2016] [Accepted: 06/17/2016] [Indexed: 11/23/2022]
Abstract
Autophagy and cellular metabolism are tightly linked processes, but how individual metabolic enzymes regulate the process of autophagy is not well understood. This study implicates ribose-5-phosphate isomerase (RPIA), a key regulator of the pentose phosphate pathway, in the control of autophagy. We used a dual gene deletion strategy, combining shRNA-mediated knockdown studies with CRISPR/Cas9 genome editing. Knockdown of RPIA by shRNA or genomic deletion by CRISPR/Cas9 genome editing, results in an increase of ATG4B-mediated LC3 processing and in the appearance of LC3-positive autophagosomes in cells. Increased LC3 processing upon knockdown of RPIA can be reversed by treatment with the antioxidant N-acetyl cysteine. The results are consistent with a model in which RPIA suppresses autophagy and LC3 processing by modulation of redox signaling. Ribose-5-phosphate isomerase links autophagy with the pentose phosphate pathway. Generation of a CRISPR/Cas9 genome edited RPIA knockout cell line RPIA isomerase suppresses cellular LC3 processing and autophagosome formation.
Collapse
|
16
|
Yang Z, Wilkie-Grantham RP, Yanagi T, Shu CW, Matsuzawa SI, Reed JC. ATG4B (Autophagin-1) phosphorylation modulates autophagy. J Biol Chem 2015; 290:26549-61. [PMID: 26378241 DOI: 10.1074/jbc.m115.658088] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Indexed: 11/06/2022] Open
Abstract
Autophagy is a catabolic cellular mechanism for entrapping cellular macromolecules and organelles in intracellular vesicles and degrading their contents by fusion with lysosomes. Important roles for autophagy have been elucidated for cell survival during nutrient insufficiency, eradication of intracellular pathogens, and counteracting aging through clearance of senescent proteins and mitochondria. Autophagic vesicles become decorated with LC3, a protein that mediates their fusion with lysosomes. LC3 is a substrate of the cysteine protease ATG4B (Autophagin-1), where cleavage generates a C-terminal glycine required for LC3 conjugation to lipids in autophagosomes. ATG4B both cleaves pro-LC3 and also hydrolyzes lipids from cleaved LC3. We show here that phosphorylation of ATG4B at Ser-383 and Ser-392 increases its hydrolyase activity as measured using LC3 as a substrate. Reconstituting atg4b(-/-) cells with phosphorylation-deficient ATG4B showed a role of ATG4B phosphorylation in LC3 delipidation and autophagic flux, thus demonstrating that the cellular activity of ATG4B is modulated by phosphorylation. Proteolytic conversion of pro-LC3 to LC3-I was not significantly impacted by ATG4B phosphorylation in cells. Phosphorylation-deficient ATG4B also showed reduced interactions with the lipid-conjugated LC3 but not unconjugated LC3. Taken together, these findings demonstrate a role for Ser-383 and Ser-392 phosphorylation of ATG4B in control of autophagy.
Collapse
Affiliation(s)
- Zhifen Yang
- From the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037, Department of Radiation Oncology, Stanford University, Palo Alto, California 94305
| | | | - Teruki Yanagi
- From the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Chih-Wen Shu
- From the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037, Department of Medical Education and Research; Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan 813, and
| | - Shu-Ichi Matsuzawa
- From the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037,
| | - John C Reed
- From the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037, Roche, Pharmaceutical Research & Early Development, Roche Innovation Center-Basel, Basel, Switzerland CH4014
| |
Collapse
|
17
|
Liu J, Li Y, Hoh J. Generation and characterization of mice with a conditional null allele of the HtrA4 gene. Mol Med Rep 2015; 12:6768-74. [PMID: 26353049 PMCID: PMC4626166 DOI: 10.3892/mmr.2015.4291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/11/2015] [Indexed: 12/19/2022] Open
Abstract
High temperature requirement factor A4 (HtrA4) is a member of the HtrA family of serine peptidases involved in regulating protein-protein interactions. Little is known regarding the function of HtrA4 in humans and in mouse models. To gain insights into the role of HtrA4 in vivo, mice were generated with a conditional null allele of HtrA4 by flanking exons 4, 5 and 6 with loxP sites. Cre-mediated recombination, using a ubiquitously active Rosa26-Cre line, resulted in the deletion of the floxed region in the mouse genome. Mice homozygous for the recombinant allele (HtrA4−/−) were viable, fertile and appeared to be normal. The HtrA4 protein was detectable in coronary vessels and in the placenta. However, the loss of HtrA4 affected neither the basic heart nor placental functions. These mice, featuring a conditional null allele of HtrA4, may provide a valuable tool to investigate the role of HtrA4 in development and pathogenesis of coronary heart disease and preeclampsia.
Collapse
Affiliation(s)
- Ju Liu
- Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
| | - Yan Li
- Children's Health Care Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Josephine Hoh
- Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
18
|
Periz G, Lu J, Zhang T, Kankel MW, Jablonski AM, Kalb R, McCampbell A, Wang J. Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription. PLoS Biol 2015; 13:e1002114. [PMID: 25837623 PMCID: PMC4383508 DOI: 10.1371/journal.pbio.1002114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 02/08/2023] Open
Abstract
Protein quality control is essential for clearing misfolded and aggregated proteins from the cell, and its failure is associated with many neurodegenerative disorders. Here, we identify two genes, ufd-2 and spr-5, that when inactivated, synergistically and robustly suppress neurotoxicity associated with misfolded proteins in Caenorhabditis elegans. Loss of human orthologs ubiquitination factor E4 B (UBE4B) and lysine-specific demethylase 1 (LSD1), respectively encoding a ubiquitin ligase and a lysine-specific demethylase, promotes the clearance of misfolded proteins in mammalian cells by activating both proteasomal and autophagic degradation machineries. An unbiased search in this pathway reveals a downstream effector as the transcription factor p53, a shared substrate of UBE4B and LSD1 that functions as a key regulator of protein quality control to protect against proteotoxicity. These studies identify a new protein quality control pathway via regulation of transcription factors and point to the augmentation of protein quality control as a wide-spectrum antiproteotoxicity strategy. A new protein quality control regulatory pathway is identified in which a ubiquitin ligase and a lysine-specific demethylase act together on the transcription factor p53 to control protein degradation systems. To function properly, proteins must assume their correct three-dimensional shapes. There are numerous mechanisms within the cell, collectively referred to as protein quality control (PQC), that verify proper folding. If abnormal folding is detected, PQC can either help the protein to refold or target it for degradation. Failures in protein folding and PQC lead to the accumulation of misfolded proteins, which often self-associate into large aggregations that are thought to be the underlying cause of several neurodegenerative diseases. In this study, we use the roundworm Caenorhabditis elegans as a model to understand how cells handle disease-associated misfolded proteins. In a large-scale genetic screen, we discovered two suppressor genes, ufd-2 and spr-5, which encode a ubiquitin ligase and a lysine-specific demethylase, respectively. When these two proteins are inactivated, we observe a marked reduction in the toxicity of several misfolded proteins. ufd-2 and spr-5 are conserved in humans (UBE4B and LSD1, respectively), as are their effects on misfolded proteins. We show that UBE4B and LSD1 regulate the activity of protein degradation machineries including the proteasome and autophagosomes. Using microarrays and biochemical analyses, we identify p53 as a key downstream transcription factor that mediates the action of UBE4B and LSD1 on protein clearance. This work establishes p53 as a regulator of proteome integrity and uncovers a new protein quality control pathway that could potentially be exploited to increase the degradation of misfolded proteins in diseased cells.
Collapse
Affiliation(s)
- Goran Periz
- Department of Biochemistry and Molecular Biology and Department of Neuroscience, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jiayin Lu
- Department of Biochemistry and Molecular Biology and Department of Neuroscience, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology and Department of Neuroscience, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Mark W. Kankel
- Biogen Idec, Cambridge, Massachusetts, United States of America
| | - Angela M. Jablonski
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert Kalb
- Department of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Jiou Wang
- Department of Biochemistry and Molecular Biology and Department of Neuroscience, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
19
|
Development of a Gaussia luciferase-based human norovirus protease reporter system: cell type-specific profile of Norwalk virus protease precursors and evaluation of inhibitors. J Virol 2014; 88:10312-26. [PMID: 25008934 DOI: 10.1128/jvi.01111-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
UNLABELLED Norwalk virus (NV) is the prototype strain of human noroviruses (HuNoVs), a group of positive-strand RNA viruses in the Caliciviridae family and the leading cause of epidemic gastroenteritis worldwide. Investigation of HuNoV replication and development of antiviral therapeutics in cell culture remain challenging tasks. Here, we present NoroGLuc, a HuNoV protease reporter system based on a fusion of NV p41 protein with a naturally secreted Gaussia luciferase (GLuc), linked by the p41/p22 cleavage site for NV protease (Pro). trans cleavage of NoroGLuc by NV Pro or Pro precursors results in release and secretion of an active GLuc. Using this system, we observed a cell type-specific activity profile of NV Pro and Pro precursors, suggesting that the activity of NV Pro is modulated by other viral proteins in the precursor forms and strongly influenced by cellular factors. NoroGLuc was also cleaved by Pro and Pro precursors generated from replication of NV stool RNA in transfected cells, resulting in a measurable increase of secreted GLuc. Truncation analysis revealed that the N-terminal membrane association domain of NV p41 is critical for NoroGLuc activity. Although designed for NV, a genogroup GI.1 norovirus, NoroGLuc also efficiently detects Pro activities from GII.3 and GII.4 noroviruses. At noncytotoxic concentrations, protease inhibitors ZnCl2 and Nα-p-tosyl-l-lysine chloromethyl ketone (TLCK) exhibited dose-dependent inhibitory effects on a GII.4 Pro by NoroGLuc assay. These results establish NoroGLuc as a pan-genogroup HuNoV protease reporter system that can be used for the study of HuNoV proteases and precursors, monitoring of viral RNA replication, and evaluation of antiviral agents. IMPORTANCE Human noroviruses are the leading cause of epidemic gastroenteritis worldwide. Currently, there are no vaccines or antiviral drugs available to counter these highly contagious viruses. These viruses are currently noncultivatable in cell culture. Here, we report the development of a novel cell-based reporter system called NoroGLuc that can be used for studying norovirus replication and also for screening/evaluation of antiviral agents. This system is based on the fusion between viral protein p41 and a naturally secreted Gaussia luciferase (GLuc) with a cleavage site that can be recognized by the viral protease. Cleavage of this fusion protein by the viral protease results in the release and secretion of an active GLuc. Using NoroGLuc, we demonstrated a cell type-specific activity profile of the viral protease and its precursors and dose-dependent inhibitory effects of two protease inhibitors. This novel reporter system should be useful in probing norovirus replication and evaluating antiviral agents.
Collapse
|
20
|
Luft C, Freeman J, Elliott D, Al-Tamimi N, Kriston-Vizi J, Heintze J, Lindenschmidt I, Seed B, Ketteler R. Application of Gaussia luciferase in bicistronic and non-conventional secretion reporter constructs. BMC BIOCHEMISTRY 2014; 15:14. [PMID: 25007711 PMCID: PMC4099409 DOI: 10.1186/1471-2091-15-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 07/05/2014] [Indexed: 11/28/2022]
Abstract
Background Secreted luciferases are highly useful bioluminescent reporters for cell-based assays and drug discovery. A variety of secreted luciferases from marine organisms have been described that harbor an N-terminal signal peptide for release along the classical secretory pathway. Here, we have characterized the secretion of Gaussia luciferase in more detail. Results We describe three basic mechanisms by which GLUC can be released from cells: first, classical secretion by virtue of the N-terminal signal peptide; second, internal signal peptide-mediated secretion and third, non-conventional secretion in the absence of an N-terminal signal peptide. Non-conventional release of dNGLUC is not stress-induced, does not require autophagy and can be enhanced by growth factor stimulation. Furthermore, we have identified the golgi-associated, gamma adaptin ear containing, ARF binding protein 1 (GGA1) as a suppressor of release of dNGLUC. Conclusions Due to its secretion via multiple secretion pathways GLUC can find multiple applications as a research tool to study classical and non-conventional secretion. As GLUC can also be released from a reporter construct by internal signal peptide-mediated secretion it can be incorporated in a novel bicistronic secretion system.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Robin Ketteler
- Medical Research Council, Laboratory for Moleclar and Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| |
Collapse
|
21
|
Antiviral signaling protein MITA acts as a tumor suppressor in breast cancer by regulating NF-κB induced cell death. Biochim Biophys Acta Mol Basis Dis 2014; 1842:144-53. [DOI: 10.1016/j.bbadis.2013.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 10/26/2013] [Accepted: 11/07/2013] [Indexed: 12/18/2022]
|
22
|
Abstract
Over the last three decades, imaging has been a thriving field with continuous egression of more reliable and highly sophisticated tools and techniques allowing better understanding of biological processes in living organisms. This field continues to expand and its applications broaden to encompass limitless applications in various biomedical research areas. It is however, of utmost importance to understand the capabilities and limitations of this technique as new challenges and hurdles continue to arise. This chapter describes the general properties of bioluminescence imaging and commonly used reporters while underlining the challenges and limitations with these modalities.
Collapse
Affiliation(s)
- Christian E Badr
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuroscience Center, Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
23
|
Kuang E, Okumura CYM, Sheffy-Levin S, Varsano T, Shu VCW, Qi J, Niesman IR, Yang HJ, López-Otín C, Yang WY, Reed JC, Broday L, Nizet V, Ronai ZA. Regulation of ATG4B stability by RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection. PLoS Genet 2012; 8:e1003007. [PMID: 23093945 PMCID: PMC3475677 DOI: 10.1371/journal.pgen.1003007] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/20/2012] [Indexed: 12/27/2022] Open
Abstract
Autophagy is the mechanism by which cytoplasmic components and organelles are degraded by the lysosomal machinery in response to diverse stimuli including nutrient deprivation, intracellular pathogens, and multiple forms of cellular stress. Here, we show that the membrane-associated E3 ligase RNF5 regulates basal levels of autophagy by controlling the stability of a select pool of the cysteine protease ATG4B. RNF5 controls the membranal fraction of ATG4B and limits LC3 (ATG8) processing, which is required for phagophore and autophagosome formation. The association of ATG4B with—and regulation of its ubiquitination and stability by—RNF5 is seen primarily under normal growth conditions. Processing of LC3 forms, appearance of LC3-positive puncta, and p62 expression are higher in RNF5−/− MEF. RNF5 mutant, which retains its E3 ligase activity but does not associate with ATG4B, no longer affects LC3 puncta. Further, increased puncta seen in RNF5−/− using WT but not LC3 mutant, which bypasses ATG4B processing, substantiates the role of RNF5 in early phases of LC3 processing and autophagy. Similarly, RNF-5 inactivation in Caenorhabditis elegans increases the level of LGG-1/LC3::GFP puncta. RNF5−/− mice are more resistant to group A Streptococcus infection, associated with increased autophagosomes and more efficient bacterial clearance by RNF5−/− macrophages. Collectively, the RNF5-mediated control of membranalATG4B reveals a novel layer in the regulation of LC3 processing and autophagy. Autophagy is an intracellular catabolic process by which a cell's own components are degraded through the lysosomal machinery. Autophagy is implicated in various cellular processes such as growth and development, cancer, and inflammation. Using biochemistry, cell biology, and genetic models, we identify a ubiquitin ligase that limits autophagy in the absence of an inducing stimulus (e.g. starvation). The control of basal autophagy is mediated by the ubiquitin ligase RNF5 through its regulation of the membrane-associated ATG4B protease. Using RNF5 mutant mice we demonstrate the implications of this regulation for host defense mechanisms that limit intracellular infection by bacterial pathogens.
Collapse
Affiliation(s)
- Ersheng Kuang
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Cheryl Y. M. Okumura
- Department of Pediatrics, School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Sharon Sheffy-Levin
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tal Varsano
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Vincent Chih-Wen Shu
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Jianfei Qi
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Ingrid R. Niesman
- Department of Anesthesiology, University of California San Diego, La Jolla, California, United States of America
- Veterans Administration San Diego Healthcare System, San Diego, California, United States of America
| | - Huei-Jiun Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Wei Yuan Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - John C. Reed
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Limor Broday
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (LB); (VN); (ZAR)
| | - Victor Nizet
- Department of Pediatrics, School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (LB); (VN); (ZAR)
| | - Ze'ev A. Ronai
- Signal Transduction and Cell Death Programs, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (LB); (VN); (ZAR)
| |
Collapse
|
24
|
Garcia-Garcia A, Rodriguez-Rocha H, Tseng MT, Montes de Oca-Luna R, Zhou HS, McMasters KM, Gomez-Gutierrez JG. E2F-1 lacking the transcriptional activity domain induces autophagy. Cancer Biol Ther 2012; 13:1091-101. [PMID: 22825328 DOI: 10.4161/cbt.21143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The transcription factor E2F-1 plays a crucial role in the control of cell proliferation. E2F-1 has tumor suppressive properties by inducing apoptosis and autophagy. In this study, E2F-1 and its truncated form (E2Ftr), lacking the transactivation domain (TAD), were compared for their ability to induce autophagy. In Gaussia luciferase-based assays, both E2F-1 and E2Ftr induced the proteolytic cleavage of the autophagic marker LC3. In addition, LC3 and autophagy protein 5 (Atg5) were upregulated by E2F-1 and E2Ftr. Likewise, both E2F proteins induced a punctate pattern of GFP-tagged LC3, indicating autophagosome formation. The presence of double-membrane autophagic vesicles induced by E2F-1 and E2Ftr was confirmed by transmission electron microscopy (TEM). The application of z-VAD-fmk, a caspase inhibitor, partially blocked both E2F-1 and E2Ftr-mediated cytotoxicity. Moreover, Atg5 (-/-) cells were more resistant to the E2F-1 or E2Ftr-induced cell killing effect than Atg5 wt cells. The TAD of E2F-1 is not essential for induction of autophagy; apoptosis and autophagy cooperate for an efficient cancer cell killing effect induced by E2F-1 or E2Ftr. E2Ftr-induced autophagy is a promising approach to destroy tumors that are resistant to conventional treatments.
Collapse
|
25
|
Li M, Chen X, Ye QZ, Vogt A, Yin XM. A high-throughput FRET-based assay for determination of Atg4 activity. Autophagy 2012; 8:401-12. [PMID: 22302004 PMCID: PMC3337841 DOI: 10.4161/auto.18777] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Atg4 is required for cleaving Atg8, allowing it to be conjugated to phosphatidylethanolamine on phagophore membranes, a key step in autophagosome biogenesis. Deconjugation of Atg8 from autophagosomal membranes could be also a regulatory step in controlling autophagy. Therefore, the activity of Atg4 is important for autophagy and could be a target for therapeutic intervention. In this study, a sensitive and specific method to measure the activity of two Atg4 homologs in mammalian cells, Atg4A and Atg4B, was developed using a fluorescence resonance energy transfer (FRET)-based approach. Thus LC3B and GATE-16, two substrates that could be differentially cleaved by Atg4A and Atg4B, were fused with CFP and YFP at the N- and C-terminus, respectively, allowing FRET to occur. The FRET signals decreased in proportion to the Atg4-mediated cleavage, which separated the two fluorescent proteins. This method is highly efficient for measuring the enzymatic activity and kinetics of Atg4A and Atg4B under in vitro conditions. Applications of the assay indicated that the activity of Atg4B was dependent on its catalytic cysteine and expression level, but showed little changes under several common autophagy conditions. In addition, the assays displayed excellent performance in high throughput format and are suitable for screening and analysis of potential modulators. In summary, the FRET-based assay is simple and easy to use, is sensitive and specific, and is suitable for both routine measurement of Atg4 activity and high-throughput screening.
Collapse
Affiliation(s)
- Min Li
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | | | | |
Collapse
|
26
|
Abstract
Over the last decade, cell-based screening has become a powerful method in target identification and plays an important role both in basic research and drug discovery. The availability of whole genome sequences and improvements in cell-based screening techniques opened new avenues for high-throughput experiments. Large libraries of RNA interference reagents available for many organisms allow the dissection of broad spectrum of cellular processes. Here, we describe the current state of the large-scale phenotype screening with a focus on cell-based screens. We underline the importance and provide details of screen design, scalability, performance, data analysis, and hit prioritization. Similar to classical high-throughput in vitro screens with defined-target approaches in the past, cell-based screens depend on a successful establishment of robust phenotypic assays, the ability to quantitatively measure phenotypic changes and bioinformatics methods for data analysis, integration, and interpretation.
Collapse
Affiliation(s)
- Kubilay Demir
- Division of Signaling and Functional Genomics, Department for Cell and Molecular Biology, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
| | | |
Collapse
|
27
|
Maguire CA, Deliolanis NC, Pike L, Niers JM, Tjon-Kon-Fat LA, Sena-Esteves M, Tannous BA. Gaussia luciferase variant for high-throughput functional screening applications. Anal Chem 2010; 81:7102-6. [PMID: 19601604 DOI: 10.1021/ac901234r] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gaussia luciferase (Gluc) is a sensitive reporter for studying different biological processes such as gene expression, promoter activity, protein-protein interactions, signal transduction, as well as tumor cell growth and response to therapy. Since Gluc is naturally secreted, the kinetics of these processes can be monitored in real-time by measuring an aliquot of conditioned medium in culture or a few microliters of blood in vivo at different time points. Gluc catalyzes light emission with a short half-life which is unfavorable for certain applications. We isolated a Gluc mutant that catalyzes enhanced light stability in the presence of a detergent, in combination with high sensitivity, making it an attractive luciferase for high-throughput functional screening applications.
Collapse
Affiliation(s)
- Casey A Maguire
- Molecular Neurogenetics Unit, Department of Neurology, Harvard Medical School, Boston Massachusetts 02115, USA
| | | | | | | | | | | | | |
Collapse
|
28
|
Ketteler R. The Feynman trajectories: determining the path of a protein using fixed-endpoint assays. ACTA ACUST UNITED AC 2010; 15:321-6. [PMID: 20130209 DOI: 10.1177/1087057109357116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Richard Feynman postulated in 1948 that the path of an electron can be best described by the sum or functional integral of all possible trajectories rather than by the notion of a single, unique trajectory. As a consequence, the position of an electron does not harbor any information about the paths that contributed to this position. This observation constitutes a classical endpoint observation. The endpoint assay is the desired type of experiment for high-throughput screening applications, mainly because of limitations in data acquisition and handling. Quite contrary to electrons, it is possible to extract information about the path of a protein using endpoint assays, and these types of applications are reviewed in this article.
Collapse
Affiliation(s)
- Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
| |
Collapse
|
29
|
Huett A, Xavier RJ. Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases. Inflamm Bowel Dis 2010; 16:152-74. [PMID: 19575363 PMCID: PMC3954538 DOI: 10.1002/ibd.20991] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Autophagy is a conserved homeostatic process by which cells degrade and recycle cytoplasmic contents and organelles. Recently, autophagy has come to prominence as a factor in many disease states, including inflammatory bowel diseases. In this review we explore the recent discoveries in autophagy and how these relate to the special conditions experienced by the gut mucosa. We will pay particular attention to autophagy as an innate immune process and its role in the development and education of the adaptive immune system.
Collapse
Affiliation(s)
- Alan Huett
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA,Gastrointestinal Unit, Center for Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Ramnik J. Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA,Gastrointestinal Unit, Center for Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| |
Collapse
|
30
|
Bioluminescent CXCL12 fusion protein for cellular studies of CXCR4 and CXCR7. Biotechniques 2009; 47:625-32. [PMID: 19594447 DOI: 10.2144/000113126] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemokine CXCL12 and its two known receptors, CXCR4 and CXCR7, may play a role in diseases including tumor growth and metastasis, atherosclerosis, and HIV infection. Therefore, these molecules may be promising targets for drug development. While studies of cell signaling and high-throughput screening for drug discovery increasingly are based on luminescent assays because of their high sensitivity and signal-to-background ratio, there currently is no bioluminescent assay for chemokine[#x02013]chemokine receptor binding. To develop a bioluminescent probe for chemokine binding and cellular uptake, we fused CXCL12 to Gaussia luciferase (GL), an ATP-independent enzyme that is the smallest known luciferase. Fusing CXCL12 to Gaussia luciferase (CXCL12-GL) did not alter the bioluminescence emission spectrum and only minimally affected enzyme function under varying conditions of pH, temperature, and NaCl concentration. CXCL12-GL also activated CXCR4-dependent signaling to a comparable extent as unfused CXCL12. Using multiwell plate assays, we established that CXCR7 increases cell-associated CXCL12 to a significantly greater extent than CXCR4. We also showed that CXCL12-GL can be used to quantify inhibition of chemokine receptor binding by compounds that specifically target CXCR7. These data validate CXCL12-GL as a bioluminescent probe to investigate molecular functions of CXCR4 and CXCR7 and screen for compounds that modulate ligand-receptor binding.
Collapse
|
31
|
Abstract
Autophagy is a cellular process that has been defined and analyzed almost entirely by qualitative measures. In no small part, this is attributable to the absence of robust quantitative assays that can easily and reliably permit the progress of key steps in autophagy to be assessed. We have recently developed a cell-based assay that specifically measures proteolytic cleavage of a tripartite sensor protein by the autophagy protease ATG4B. Activation of ATG4B results in release of Gaussia luciferase from cells that can be non-invasively harvested from cellular supernatants. Here, we compare this technique to existing methods and propose that this type of assay will be suitable for genome-wide functional screens and in vivo analysis of autophagy.
Collapse
Affiliation(s)
- Robin Ketteler
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
| | | |
Collapse
|