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A conserved ankyrin repeat-containing protein regulates conoid stability, motility and cell invasion in Toxoplasma gondii. Nat Commun 2017; 8:2236. [PMID: 29269729 PMCID: PMC5740107 DOI: 10.1038/s41467-017-02341-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/22/2017] [Indexed: 11/08/2022] Open
Abstract
Apicomplexan parasites are typified by an apical complex that contains a unique microtubule-organizing center (MTOC) that organizes the cytoskeleton. In apicomplexan parasites such as Toxoplasma gondii, the apical complex includes a spiral cap of tubulin-rich fibers called the conoid. Although described ultrastructurally, the composition and functions of the conoid are largely unknown. Here, we localize 11 previously undescribed apical proteins in T. gondii and identify an essential component named conoid protein hub 1 (CPH1), which is conserved in apicomplexan parasites. CPH1 contains ankyrin repeats that are required for structural integrity of the conoid, parasite motility, and host cell invasion. Proximity labeling and protein interaction network analysis reveal that CPH1 functions as a hub linking key motor and structural proteins that contain intrinsically disordered regions and coiled coil domains. Our findings highlight the importance of essential protein hubs in controlling biological networks of MTOCs in early-branching protozoan parasites. Apicomplexan parasites such as Toxoplasma gondii possess a tubulin-rich structure called the conoid. Here, Long et al. identify a conoid protein that interacts with motor and structural proteins and is required for structural integrity of the conoid, parasite motility, and host cell invasion.
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Spadaro D, Le S, Laroche T, Mean I, Jond L, Yan J, Citi S. Tension-Dependent Stretching Activates ZO-1 to Control the Junctional Localization of Its Interactors. Curr Biol 2017; 27:3783-3795.e8. [PMID: 29199076 DOI: 10.1016/j.cub.2017.11.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/27/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Tensile forces regulate epithelial homeostasis, but the molecular mechanisms behind this regulation are poorly understood. Using structured illumination microscopy and proximity ligation assays, we show that the tight junction protein ZO-1 exists in stretched and folded conformations within epithelial cells, depending on actomyosin-generated force. We also show that ZO-1 and ZO-2 regulate the localization of the transcription factor DbpA and the tight junction membrane protein occludin in a manner that depends on the organization of the actin cytoskeleton, myosin-II activity, and substrate stiffness, resulting in modulation of gene expression, cell proliferation, barrier function, and cyst morphogenesis. Pull-down experiments show that interactions between N-terminal (ZPSG) and C-terminal domains of ZO-1 prevent binding of DbpA to the ZPSG, suggesting that force-dependent intra-molecular interactions regulate ZPSG binding to ligands within cells. In vivo and in vitro experiments also suggest that ZO-1 heterodimerization with ZO-2 promotes the stretched conformation and ZPSG interaction with ligands. Magnetic tweezers single-molecule experiments suggest that pN-scale tensions (∼2-4 pN) are sufficient to maintain the stretched conformation of ZO-1, while keeping its structured domains intact, and that 5-20 pN force is required to disrupt the interaction between the extreme C-terminal and the ZPSG domains of ZO-1. We propose that tensile forces regulate epithelial homeostasis by activating ZO proteins through stretching, to control the junctional recruitment and downstream signaling of their interactors.
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Affiliation(s)
- Domenica Spadaro
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland
| | - Shimin Le
- Department of Physics, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore; Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Thierry Laroche
- EPFL School of Life Sciences PTBIOP, Station 19, 1015 Lausanne, Switzerland
| | - Isabelle Mean
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland
| | - Lionel Jond
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland
| | - Jie Yan
- Department of Physics, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore; Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Sandra Citi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland.
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53
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Fredriksson-Lidman K, Van Itallie CM, Tietgens AJ, Anderson JM. Sorbin and SH3 domain-containing protein 2 (SORBS2) is a component of the acto-myosin ring at the apical junctional complex in epithelial cells. PLoS One 2017; 12:e0185448. [PMID: 28961272 PMCID: PMC5621683 DOI: 10.1371/journal.pone.0185448] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022] Open
Abstract
SORBS2 is a scaffolding protein associated with Abl/Arg non-receptor tyrosine kinase pathways and is known to interact with actin and several other cytoskeletal proteins in various cell types. Previous BioID proximity labeling of tight and adherens junction proteins suggested that SORBS2 is a component of the apical junction complex of epithelial cells. We asked whether SORBS2 plays a previously unappreciated role in controlling perijunctional actin and tight junction barrier function. Using super resolution imaging we confirmed that SORBS2 is localized at the apical junction complex but farther from the membrane than ZO-1 and located partially overlapping both the tight- and adherens junctions with a periodic concentration that alternates with myosin IIB in polarized epithelial cells. Overexpression of GFP-SORBS2 recruited alpha-actinin, vinculin and N-WASP, and possibly CIP4 to cellular junctions. However, CRISPR-Cas9 knock-out of SORBS2 did not alter the localization- or immunofluorescent staining intensity of these or several other junctional- and cytoskeletal proteins. SORBS2 knock-out also did not affect the barrier function as measured by TER and dextran flux; nor did it change actin-dependent junction re-assembly as measured by Ca2+-switch and Latrunculin-B wash-out assays. The kinetics of HGF-induced cell scattering and wound healing, and dextran flux increase induced by PDGF also were unaffected by SORBS2 knock-out. SORBS2 concentrates with apical junctional actin that accumulates in response to knock-down of ZO-1 and ZO-2. In spite of our finding that SORBS2 is clearly a component of the apical junction complex, it does not appear to be required for either normal tight- or adherens junction assembly, structure or function or for growth factor-mediated changes in tight junction dynamics.
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Affiliation(s)
- Karin Fredriksson-Lidman
- Laboratory of Tight Junction Structure and Function, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Christina M. Van Itallie
- Laboratory of Tight Junction Structure and Function, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Amber J. Tietgens
- Laboratory of Tight Junction Structure and Function, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James M. Anderson
- Laboratory of Tight Junction Structure and Function, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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54
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Li XJ, Mu YM, Qin QF, Zeng ZX, Li YS, Zhang WK, Tang HB, Tian GH, Shang HC. Chronic high-dosage fish oil exacerbates gut-liver axis injury in alcoholic steatohepatitis in mice: the roles of endotoxin and IL-4 in Kupffer cell polarization imbalance. Toxicol Res (Camb) 2017; 6:611-620. [PMID: 30090529 DOI: 10.1039/c7tx00037e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 01/21/2023] Open
Abstract
In the present study, intestinal tight junctions (TJs) and Kupffer cell polarization were investigated in an alcoholic steatohepatitis (ASH) mouse model to uncover the potential side effects of overexposure to fish oil or omega-3 fatty acids. The mice were fed ad libitum with a liquid diet containing ethanol and fish oil. In the meantime, ethanol was given every 5-7 days by gavage to simulate binge drinking. After the 7th binge, steatosis, necrosis, inflammatory infiltration, and bridging fibrosis were observed in the liver by histological staining. After the 13th binge, the inducers, markers and other downstream genes/proteins of the Kupffer cell M1/M2 phenotype in the liver, serum, and small intestine were analysed. The results suggested that a chronic high dosage of fish oil alone reduced the mRNA levels of most genes tested and showed a tendency to damage the intestinal zonula occludens-1 localization and reduce the number of M2 Kupffer cells. Meanwhile, the combination of fish oil and ethanol damaged the intestinal TJs, resulting in an increased endotoxin level in the liver. Gut-derived endotoxin polarized Kupffer cells to the M1 phenotype, whereas the number of cells with the M2 phenotype (markers: CD163 and CD206) was decreased. Interleukin-4 (IL-4), an M2 Kupffer cell inducer, was also decreased. Moreover, in vitro experiments showed that IL-4 reversed eicosapentaenoic acid-induced CD163 and CD206 mRNA suppression in RAW 264.7 cells. Overall, our results showed that a chronic high dosage of fish oil exacerbated gut-liver axis injury in alcoholic liver disease in mice, and endotoxin/IL-4-induced Kupffer cell polarization imbalance might play an important role in that process.
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Affiliation(s)
- Xiao-Jun Li
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - Yun-Mei Mu
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - Qiu-Fang Qin
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - Zi-Xuan Zeng
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - Yu-Sang Li
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - Wei Kevin Zhang
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332
| | - He-Bin Tang
- Department of Pharmacology , School of Pharmaceutical Sciences , South-Central University for Nationalities , No. 182 Minyuan Road , 430074 , Wuhan , China . ; ; Tel: +86 27 6784 2332.,Key Laboratory of Chinese Internal Medicine of MOE and Beijing , Dongzhimen Hospital , Beijing University of Chinese Medicine , 100029 , Beijing , China . ; ; Tel: +86 10 8401 2510.,Research Institute of Huazhong University of Science and Technology in Shenzhen , 518057 , Shenzhen , China
| | - Gui-Hua Tian
- Key Laboratory of Chinese Internal Medicine of MOE and Beijing , Dongzhimen Hospital , Beijing University of Chinese Medicine , 100029 , Beijing , China . ; ; Tel: +86 10 8401 2510
| | - Hong-Cai Shang
- Key Laboratory of Chinese Internal Medicine of MOE and Beijing , Dongzhimen Hospital , Beijing University of Chinese Medicine , 100029 , Beijing , China . ; ; Tel: +86 10 8401 2510
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55
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Yano T, Kanoh H, Tamura A, Tsukita S. Apical cytoskeletons and junctional complexes as a combined system in epithelial cell sheets. Ann N Y Acad Sci 2017; 1405:32-43. [DOI: 10.1111/nyas.13432] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Tomoki Yano
- Laboratory of Biological Science, Graduate School of Frontier Biosciences and Graduate School of Medicine; Osaka University; Osaka Japan
| | - Hatsuho Kanoh
- Laboratory of Biological Science, Graduate School of Frontier Biosciences and Graduate School of Medicine; Osaka University; Osaka Japan
- Graduate School of Biostudies; Kyoto University; Kyoto Japan
| | - Atsushi Tamura
- Laboratory of Biological Science, Graduate School of Frontier Biosciences and Graduate School of Medicine; Osaka University; Osaka Japan
| | - Sachiko Tsukita
- Laboratory of Biological Science, Graduate School of Frontier Biosciences and Graduate School of Medicine; Osaka University; Osaka Japan
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56
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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57
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Arnold TR, Stephenson RE, Miller AL. Rho GTPases and actomyosin: Partners in regulating epithelial cell-cell junction structure and function. Exp Cell Res 2017; 358:20-30. [PMID: 28363828 DOI: 10.1016/j.yexcr.2017.03.053] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/25/2017] [Accepted: 03/27/2017] [Indexed: 01/11/2023]
Abstract
Epithelial tissues are defined by polarized epithelial cells that are integrated into tissues and exhibit barrier function in order to regulate what is allowed to pass between cells. Cell-cell junctions must be stable enough to promote barrier function and tissue integrity, yet plastic enough to remodel when necessary. This remarkable ability to dynamically sense and respond to changes in cell shape and tissue tension allows cell-cell junctions to remain functional during events that disrupt epithelial homeostasis including morphogenesis, wound healing, and cell division. In order to achieve this plasticity, both tight junctions and adherens junctions are coupled to the underlying actomyosin cytoskeleton. Here, we discuss the importance of the junctional linkage to actomyosin and how a localized zone of active RhoA along with other Rho GTPases work together to orchestrate junctional actomyosin dynamics. We focus on how scaffold proteins help coordinate Rho GTPases, their upstream regulators, and their downstream effectors for efficient, localized Rho GTPase signaling output. Additionally, we highlight important roles junctional actin-binding proteins play in addition to their traditional roles in organizing actin. Together, Rho GTPases, their regulators, and effectors form compartmentalized signaling modules that regulate actomyosin structure and contractility to achieve proper cell-cell adhesion and tissue barriers.
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Affiliation(s)
- Torey R Arnold
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Rachel E Stephenson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Ann L Miller
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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58
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Contributions of intestinal epithelial barriers to health and disease. Exp Cell Res 2017; 358:71-77. [PMID: 28342899 DOI: 10.1016/j.yexcr.2017.03.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/16/2017] [Indexed: 12/15/2022]
Abstract
A core function of epithelia is to form barriers that separate tissue compartments within complex organisms. These barriers also separate the internal milieu from the external environment and are, therefore, an essential component of host defense. However, in many cases, a perfect barrier would be improbable with life itself. Examples include the air spaces within the lungs, the renal tubules, and the intestines. Here, we focus on the mechanisms by which barriers are assembled, maintained, and regulated in the context of health and disease. Because of its unique challenges and extensive study, we focus on the gastrointestinal tract as an organ-specific example of the essential contributions of the paracellular barrier to life.
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59
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Tight junction protein ZO-1 controls organic cation/carnitine transporter OCTN2 (SLC22A5) in a protein kinase C-dependent way. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:797-805. [PMID: 28257821 DOI: 10.1016/j.bbamcr.2017.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/07/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
OCTN2 (SLC22A5) is an organic cation/carnitine transporter belonging to the solute carrier transporters (SLC) family. OCTN2 is ubiquitously expressed and its presence was shown in various brain cells, including the endothelial cells forming blood-brain barrier, where it was mainly detected at abluminal membrane and in proximity of tight junctions (TJ). Since OCTN2 contains a PDZ-binding domain, the present study was focused on a possible role of transporter interaction with a TJ-associated protein ZO-1, containing PDZ domains and detected in rat Octn2 proteome. We showed previously that activation of protein kinase C (PKC) in rat astrocytes regulates Octn2 surface presence and activity. Regulation of a wild type Octn2 and its deletion mutant without a PDZ binding motif were studied in heterologous expression system in HEK293 cells. Plasma membrane presence of overexpressed Octn2 did not depend on either PKC activation or presence of PDZ-binding motif, anyhow, as assayed in proximity ligation assay, the truncation of PDZ binding motif resulted in a strongly diminished Octn2/ZO-1 interaction and in a decreased transporter activity. The same effects on Octn2 activity were detected upon PKC activation, what correlated with ZO-1 phosphorylation. It is postulated that ZO-1, when not phosphorylated by PKC, keeps Octn2 in an active state, while elimination of this binding in ΔPDZ mutant or after ZO-1 phosphorylation leads to diminution of Octn2 activity.
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60
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Kaufmann T, Kukolj E, Brachner A, Beltzung E, Bruno M, Kostrhon S, Opravil S, Hudecz O, Mechtler K, Warren G, Slade D. SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation. J Cell Sci 2016; 129:4607-4621. [PMID: 27875273 PMCID: PMC5201015 DOI: 10.1242/jcs.192633] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/09/2016] [Indexed: 12/18/2022] Open
Abstract
Sirtuin 2 (SIRT2) is an NAD-dependent deacetylase known to regulate microtubule dynamics and cell cycle progression. SIRT2 has also been implicated in the pathology of cancer, neurodegenerative diseases and progeria. Here, we show that SIRT2 depletion or overexpression causes nuclear envelope reassembly defects. We link this phenotype to the recently identified regulator of nuclear envelope reassembly ANKLE2. ANKLE2 acetylation at K302 and phosphorylation at S662 are dynamically regulated throughout the cell cycle by SIRT2 and are essential for normal nuclear envelope reassembly. The function of SIRT2 therefore extends beyond the regulation of microtubules to include the regulation of nuclear envelope dynamics.
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Affiliation(s)
- Tanja Kaufmann
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria.,Department of Molecular Biotechnology, University of Applied Sciences FH Campus Wien, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria
| | - Eva Kukolj
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Andreas Brachner
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Etienne Beltzung
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Melania Bruno
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Susanne Opravil
- Institute of Molecular Pathology, Dr Bohr-Gasse 7, Vienna 1030, Austria
| | - Otto Hudecz
- Institute of Molecular Pathology, Dr Bohr-Gasse 7, Vienna 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology, Dr Bohr-Gasse 7, Vienna 1030, Austria
| | - Graham Warren
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
| | - Dea Slade
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna 1030, Austria
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61
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Odenwald MA, Choi W, Buckley A, Shashikanth N, Joseph NE, Wang Y, Warren MH, Buschmann MM, Pavlyuk R, Hildebrand J, Margolis B, Fanning AS, Turner JR. ZO-1 interactions with F-actin and occludin direct epithelial polarization and single lumen specification in 3D culture. J Cell Sci 2016; 130:243-259. [PMID: 27802160 DOI: 10.1242/jcs.188185] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
Epithelia within tubular organs form and expand lumens. Failure of these processes can result in serious developmental anomalies. Although tight junction assembly is crucial to epithelial polarization, the contribution of specific tight junction proteins to lumenogenesis is undefined. Here, we show that ZO-1 (also known as TJP1) is necessary for the formation of single lumens. Epithelia lacking this tight junction scaffolding protein form cysts with multiple lumens and are defective in the earliest phases of polarization, both in two and three dimensions. Expression of ZO-1 domain-deletion mutants demonstrated that the actin-binding region and U5-GuK domain are crucial to single lumen development. For actin-binding region, but not U5-GuK domain, mutants, this could be overcome by strong polarization cues from the extracellular matrix. Analysis of the U5-GuK binding partners shroom2, α-catenin and occludin showed that only occludin deletion led to multi-lumen cysts. Like ZO-1-deficiency, occludin deletion led to mitotic spindle orientation defects. Single lumen formation required the occludin OCEL domain, which binds to ZO-1. We conclude that ZO-1-occludin interactions regulate multiple phases of epithelial polarization by providing cell-intrinsic signals that are required for single lumen formation.
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Affiliation(s)
- Matthew A Odenwald
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Wangsun Choi
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Aaron Buckley
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nitesh Shashikanth
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nora E Joseph
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, NorthShore University Health System, Evanston, IL 60201, USA
| | - Yitang Wang
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Michael H Warren
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Mary M Buschmann
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Roman Pavlyuk
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey Hildebrand
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ben Margolis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan S Fanning
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jerrold R Turner
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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62
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Filling the Void: Proximity-Based Labeling of Proteins in Living Cells. Trends Cell Biol 2016; 26:804-817. [PMID: 27667171 DOI: 10.1016/j.tcb.2016.09.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022]
Abstract
There are inherent limitations with traditional methods to study protein behavior or to determine the constituency of proteins in discrete subcellular compartments. In response to these limitations, several methods have recently been developed that use proximity-dependent labeling. By fusing proteins to enzymes that generate reactive molecules, most commonly biotin, proximate proteins are covalently labeled to enable their isolation and identification. In this review we describe current methods for proximity-dependent labeling in living cells and discuss their applications and future use in the study of protein behavior.
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63
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Varnaitė R, MacNeill SA. Meet the neighbors: Mapping local protein interactomes by proximity-dependent labeling with BioID. Proteomics 2016; 16:2503-2518. [PMID: 27329485 PMCID: PMC5053326 DOI: 10.1002/pmic.201600123] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 06/16/2016] [Indexed: 12/13/2022]
Abstract
Proximity-dependent biotin identification (BioID) is a recently developed method that allows the identification of proteins in the close vicinity of a protein of interest in living cells. BioID relies on fusion of the protein of interest with a mutant form of the biotin ligase enzyme BirA (BirA*) that is capable of promiscuously biotinylating proximal proteins irrespective of whether these interact directly or indirectly with the fusion protein or are merely located in the same subcellular neighborhood. The covalent addition of biotin allows the labeled proteins to be purified from cell extracts on the basis of their affinity for streptavidin and identified by mass spectrometry. To date, BioID has been successfully applied to study a variety of proteins and processes in mammalian cells and unicellular eukaryotes and has been shown to be particularly suited to the study of insoluble or inaccessible cellular structures and for detecting weak or transient protein associations. Here, we provide an introduction to BioID, together with a detailed summary of where and how the method has been applied to date, and briefly discuss technical aspects involved in the planning and execution of a BioID study.
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Affiliation(s)
- Renata Varnaitė
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK
| | - Stuart A MacNeill
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK.
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64
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Abstract
Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics' data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.
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Affiliation(s)
- Virja Mehta
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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Kiptoo P, Calcagno AM, Siahaan TJ. Physiological, Biochemical, and Chemical Barriers to Oral Drug Delivery. Drug Deliv 2016. [DOI: 10.1002/9781118833322.ch2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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66
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Kim DI, Jensen SC, Noble KA, Kc B, Roux KH, Motamedchaboki K, Roux KJ. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell 2016; 27:1188-96. [PMID: 26912792 PMCID: PMC4831873 DOI: 10.1091/mbc.e15-12-0844] [Citation(s) in RCA: 514] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/16/2016] [Indexed: 12/20/2022] Open
Abstract
A smaller promiscuous biotin ligase for proximity biotinylation called BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, exhibits enhanced labeling of proximate proteins, and demonstrates the use of a flexible linker to modulate the biotin-labeling radius. The BioID method uses a promiscuous biotin ligase to detect protein–protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein–protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
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Affiliation(s)
- Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Samuel C Jensen
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Birendra Kc
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Khatereh Motamedchaboki
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104 Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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Huang C, Wang JJ, Jing G, Li J, Jin C, Yu Q, Falkowski MW, Zhang SX. Erp29 Attenuates Cigarette Smoke Extract-Induced Endoplasmic Reticulum Stress and Mitigates Tight Junction Damage in Retinal Pigment Epithelial Cells. Invest Ophthalmol Vis Sci 2016; 56:6196-207. [PMID: 26431474 DOI: 10.1167/iovs.15-16795] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
PURPOSE Endoplasmic reticulum protein 29 (ERp29) is a novel chaperone that was recently found decreased in human retinas with AMD. Herein, we examined the effect of ERp29 on cigarette smoke-induced RPE apoptosis and tight junction disruption. METHODS Cultured human RPE (HRPE) cells (ARPE-19) or mouse RPE eyecup explants were exposed to cigarette smoke extract (CSE) for short (up to 24 hours) or long (up to 3 weeks) periods. Expression of ERp29 was up- and downregulated by adenovirus and siRNA, respectively. Endoplasmic reticulum stress markers, apoptosis, and cell death, the expression and distribution of tight junction protein ZO-1, transepithelial electrical resistance (TEER), and F-actin expression were examined. RESULTS Endoplasmic reticulum protein 29 was significantly increased by short-term exposure to CSE in ARPE-19 cells or eyecup explants but was reduced after 3-week exposure. Overexpression of ERp29 increased the levels of GRP78, p58(IPK), and Nrf-2, while reducing p-eIF2α and C/EBP homologous protein (CHOP), and protected RPE cells from CSE-induced apoptosis. In contrast, knockdown of ERp29 decreased the levels of p58(IPK) and Nrf2, but increased p-eIF2α and CHOP and exacerbated CSE-triggered cell death. In addition, overexpression of ERp29 attenuated CSE-induced reduction in ZO-1 and enhanced the RPE barrier function, as measured by TEER. Knockdown of ERp29 decreased the level of ZO-1 protein. These effects were associated with changes in the expression of cytoskeleton F-actin. CONCLUSIONS Endoplasmic reticulum protein 29 attenuates CSE-induced ER stress and enhances cell viability and barrier integrity of RPE cells, and therefore may act as a protective mechanism for RPE survival and activity.
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Affiliation(s)
- Chuangxin Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China 2Departments of Ophthalmology and Biochemistry, Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, New York, United
| | - Joshua J Wang
- Departments of Ophthalmology and Biochemistry, Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, New York, United States 3SUNY Eye Institute, State University of New York, Buffalo, New York, United States 4Department of Med
| | - Guangjun Jing
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Junhua Li
- Departments of Ophthalmology and Biochemistry, Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, New York, United States 3SUNY Eye Institute, State University of New York, Buffalo, New York, United States
| | - Chenjin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiang Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Marek W Falkowski
- Departments of Ophthalmology and Biochemistry, Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, New York, United States
| | - Sarah X Zhang
- Departments of Ophthalmology and Biochemistry, Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, New York, United States 3SUNY Eye Institute, State University of New York, Buffalo, New York, United States
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Abstract
The nuclear envelope (NE) is a critical cellular structure whose constituents and roles in a myriad of cellular processes seem ever expanding. To determine the underlying mechanisms by which the NE constituents participate in various cellular events, it is necessary to understand the nature of their protein-protein associations. BioID (proximity-dependent biotin identification) is a recently established method to generate a history of protein-protein associations as they occur over time in living cells. BioID is based on fusion of a bait protein to a promiscuous biotin ligase. Expression of the BioID fusion protein in a relevant cellular environment enables biotinylation of vicinal and interacting proteins of the bait protein, permitting isolation and identification by conventional biotin-affinity capture and mass-spec analysis. In this way, BioID provides unique capabilities to identify protein-protein associations at the NE. In this chapter we provide a detailed protocol for the application of BioID to the study of NE proteins.
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Affiliation(s)
- Dae In Kim
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Samuel C Jensen
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Kyle J Roux
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA.
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69
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Fu Y, Lv P, Yan G, Fan H, Cheng L, Zhang F, Dang Y, Wu H, Wen B. MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. Sci Rep 2015; 5:17186. [PMID: 26603343 PMCID: PMC4658601 DOI: 10.1038/srep17186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
In the interphase nucleus, chromatin is organized into three-dimensional conformation to coordinate genome functions. The lamina-chromatin association is important to facilitate higher-order chromatin in mammalian cells, but its biological significances and molecular mechanisms remain poorly understood. One obstacle is that the list of lamina-associated proteins remains limited, presumably due to the inherent insolubility of lamina proteins. In this report, we identified 182 proteins associated with lamin B1 (a constitutive component of lamina) in mouse hepatocytes, by adopting virus-based proximity-dependent biotin identification. These proteins are functionally related to biological processes such as chromatin organization. As an example, we validated the association between lamin B1 and core histone macroH2A1, a histone associated with repressive chromatin. Furthermore, we mapped Lamina-associated domains (LADs) in mouse liver cells and found that boundaries of LADs are enriched for macroH2A. More interestingly, knocking-down of macroH2A1 resulted in the release of heterochromatin foci marked by histone lysine 9 trimethylation (H3K9me3) and the decondensation of global chromatin structure. However, down-regulation of lamin B1 led to redistribution of macroH2A1. Taken together, our data indicated that macroH2A1 is associated with lamina and is required to maintain chromatin architecture in mouse liver cells.
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Affiliation(s)
- Yuhua Fu
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Pin Lv
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai, 200433
| | - Hui Fan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lu Cheng
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yongjun Dang
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Bo Wen
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
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70
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Batsios P, Meyer I, Gräf R. Proximity-Dependent Biotin Identification (BioID) in Dictyostelium Amoebae. Methods Enzymol 2015; 569:23-42. [PMID: 26778551 DOI: 10.1016/bs.mie.2015.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The identification of a bona fide lamin-like protein in Dictyostelium made this lower eukaryote an attractive model organism to study evolutionarily conserved nuclear envelope (NE) proteins important for nuclear organization and human laminopathies. Proximity-dependent biotin identification (BioID), reported by Roux and colleagues, is a powerful discovery tool for lamin-associated proteins. In this method, living cells express a bait protein (e.g., lamin) fused to an R118G-mutated version of BirA, an Escherichia coli biotinylase. In the presence of biotin, BirA-R118G biotinylates target proteins in close proximity in vivo, which are purified using streptavidin and identified by immunoblotting or mass spectrometry. We adapted the BioID method for use in Dictyostelium amoebae. The protocols described here successfully revealed Dictyostelium lamin-like protein NE81 proximity to Sun1, a conserved inner nuclear membrane protein.
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Affiliation(s)
- Petros Batsios
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany
| | - Irene Meyer
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Gräf
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany.
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71
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Abstract
A- and B-type lamins support the nuclear envelope, contribute to heterochromatin organization, and regulate a myriad of nuclear processes. The mechanisms by which lamins function in different cell types and the mechanisms by which lamin mutations cause over a dozen human diseases (laminopathies) remain unclear. The identification of proteins associated with lamins is likely to provide fundamental insight into these mechanisms. BioID (proximity-dependent biotin identification) is a unique and powerful method for identifying protein-protein and proximity-based interactions in living cells. BioID utilizes a mutant biotin ligase from bacteria that is fused to a protein of interest (bait). When expressed in living cells and stimulated with excess biotin, this BioID-fusion protein promiscuously biotinylates directly interacting and vicinal endogenous proteins. Following biotin-affinity capture, the biotinylated proteins can be identified using mass spectrometry. BioID thus enables screening for physiologically relevant protein associations that occur over time in living cells. BioID is applicable to insoluble proteins such as lamins that are often refractory to study by other methods and can identify weak and/or transient interactions. We discuss the use of BioID to elucidate novel lamin-interacting proteins and its applications in a broad range of biological systems, and provide detailed protocols to guide new applications.
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Affiliation(s)
- Aaron A Mehus
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Ruthellen H Anderson
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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72
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Van Itallie CM, Tietgens AJ, Krystofiak E, Kachar B, Anderson JM. A complex of ZO-1 and the BAR-domain protein TOCA-1 regulates actin assembly at the tight junction. Mol Biol Cell 2015; 26:2769-87. [PMID: 26063734 PMCID: PMC4571337 DOI: 10.1091/mbc.e15-04-0232] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/05/2015] [Indexed: 02/06/2023] Open
Abstract
An alternative splice in TOCA-1 targets it to tight junctions. KO of TOCA-1 results in increased flux and decreased tight junction membrane dynamics. Ultrastructural analysis shows actin accumulation at the adherens junction. Identification of the ZO-1/TOCA-1 complex provides insights into tight junction barrier dependence on the dynamic nature of cell–cell contacts and junctional actin. Assembly and sealing of the tight junction barrier are critically dependent on the perijunctional actin cytoskeleton, yet little is known about physical and functional links between barrier-forming proteins and actin. Here we identify a novel functional complex of the junction scaffolding protein ZO-1 and the F-BAR–domain protein TOCA-1. Using MDCK epithelial cells, we show that an alternative splice of TOCA-1 adds a PDZ-binding motif, which binds ZO-1, targeting TOCA-1 to barrier contacts. This isoform of TOCA-1 recruits the actin nucleation–promoting factor N-WASP to tight junctions. CRISPR-Cas9–mediated knockout of TOCA-1 results in increased paracellular flux and delayed recovery in a calcium switch assay. Knockout of TOCA-1 does not alter FRAP kinetics of GFP ZO-1 or occludin, but longer term (12 h) time-lapse microscopy reveals strikingly decreased tight junction membrane contact dynamics in knockout cells compared with controls. Reexpression of TOCA-1 with, but not without, the PDZ-binding motif rescues both altered flux and membrane contact dynamics. Ultrastructural analysis shows actin accumulation at the adherens junction in TOCA-1–knockout cells but unaltered freeze-fracture fibril morphology. Identification of the ZO-1/TOCA-1 complex provides novel insights into the underappreciated dependence of the barrier on the dynamic nature of cell-to-cell contacts and perijunctional actin.
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Affiliation(s)
- Christina M Van Itallie
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Amber Jean Tietgens
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Evan Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
| | - James M Anderson
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
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73
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Coyaud E, Mis M, Laurent EMN, Dunham WH, Couzens AL, Robitaille M, Gingras AC, Angers S, Raught B. BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 Ligase Substrates. Mol Cell Proteomics 2015; 14:1781-95. [PMID: 25900982 DOI: 10.1074/mcp.m114.045658] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 11/06/2022] Open
Abstract
The identification of ubiquitin E3 ligase substrates has been challenging, due in part to low-affinity, transient interactions, the rapid degradation of targets and the inability to identify proteins from poorly soluble cellular compartments. SCF(β-TrCP1) and SCF(β-TrCP2) are well-studied ubiquitin E3 ligases that target substrates for proteasomal degradation, and play important roles in Wnt, Hippo, and NFκB signaling. Combining 26S proteasome inhibitor (MG132) treatment with proximity-dependent biotin labeling (BioID) and semiquantitative mass spectrometry, here we identify SCF(β-TrCP1/2) interacting partners. Based on their enrichment in the presence of MG132, our data identify over 50 new putative SCF(β-TrCP1/2) substrates. We validate 12 of these new substrates and reveal previously unsuspected roles for β-TrCP in the maintenance of nuclear membrane integrity, processing (P)-body turnover and translational control. Together, our data suggest that β-TrCP is an important hub in the cellular stress response. The technique presented here represents a complementary approach to more standard IP-MS methods and should be broadly applicable for the identification of substrates for many ubiquitin E3 ligases.
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Affiliation(s)
- Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network
| | - Monika Mis
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto
| | | | - Wade H Dunham
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
| | - Amber L Couzens
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
| | - Melanie Robitaille
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto
| | - Anne-Claude Gingras
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital; ‖Department of Molecular Genetics, University of Toronto
| | - Stephane Angers
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto; **Department of Biochemistry, University of Toronto
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network; ‡‡Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
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74
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Ueda S, Blee AM, Macway KG, Renner DJ, Yamada S. Force dependent biotinylation of myosin IIA by α-catenin tagged with a promiscuous biotin ligase. PLoS One 2015; 10:e0122886. [PMID: 25806963 PMCID: PMC4373798 DOI: 10.1371/journal.pone.0122886] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 02/24/2015] [Indexed: 11/29/2022] Open
Abstract
Tissues and organs undergo constant physical perturbations and individual cells must respond to mechanical forces to maintain tissue integrity. However, molecular interactions underlying mechano-transduction are not fully defined at cell-cell junctions. This is in part due to weak and transient interactions that are likely prevalent in force-induced protein complexes. Using in situ proximal biotinylation by the promiscuous biotin ligase BirA tagged to α-catenin and a substrate stretch cell chamber, we sought to identify force-dependent molecular interactions surrounding α-catenin, an actin regulator at the sites of cadherin mediated cell-cell adhesion. While E-cadherin, β-catenin, vinculin and actin localize with α-catenin at cell-cell contacts in immuno-fluorescent staining, only β-catenin and plakoglobin were biotinylated, suggesting that this proximal biotinylation is limited to the molecules that are in the immediate vicinity of α-catenin. In mechanically stretched samples, increased biotinylation of non-muscle myosin IIA, but not myosin IIB, suggests close spatial proximity between α-catenin and myosin IIA during substrate stretching. This force-induced biotinylation diminished as myosin II activity was inhibited by blebbistatin. Taken together, this promising technique enables us to identify force sensitive complexes that may be essential for mechano-responses in force bearing cell adhesion.
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Affiliation(s)
- Shuji Ueda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Alexandra M. Blee
- Department of Biomedical Engineering, University of California Davis, Davis, CA, 95616, United States of America
| | - Katherine G. Macway
- Department of Biomedical Engineering, University of California Davis, Davis, CA, 95616, United States of America
| | - Derrick J. Renner
- Department of Biomedical Engineering, University of California Davis, Davis, CA, 95616, United States of America
| | - Soichiro Yamada
- Department of Biomedical Engineering, University of California Davis, Davis, CA, 95616, United States of America
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75
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Proteomic analysis of proteins surrounding occludin and claudin-4 reveals their proximity to signaling and trafficking networks. PLoS One 2015; 10:e0117074. [PMID: 25789658 PMCID: PMC4366163 DOI: 10.1371/journal.pone.0117074] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/18/2014] [Indexed: 01/15/2023] Open
Abstract
Tight junctions are complex membrane structures that regulate paracellular movement of material across epithelia and play a role in cell polarity, signaling and cytoskeletal organization. In order to expand knowledge of the tight junction proteome, we used biotin ligase (BioID) fused to occludin and claudin-4 to biotinylate their proximal proteins in cultured MDCK II epithelial cells. We then purified the biotinylated proteins on streptavidin resin and identified them by mass spectrometry. Proteins were ranked by relative abundance of recovery by mass spectrometry, placed in functional categories, and compared not only among the N- and C- termini of occludin and the N-terminus of claudin-4, but also with our published inventory of proteins proximal to the adherens junction protein E-cadherin and the tight junction protein ZO-1. When proteomic results were analyzed, the relative distribution among functional categories was similar between occludin and claudin-4 proximal proteins. Apart from already known tight junction- proteins, occludin and claudin-4 proximal proteins were enriched in signaling and trafficking proteins, especially endocytic trafficking proteins. However there were significant differences in the specific proteins comprising the functional categories near each of the tagging proteins, revealing spatial compartmentalization within the junction complex. Taken together, these results expand the inventory of known and unknown proteins at the tight junction to inform future studies of the organization and physiology of this complex structure.
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76
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Mojica SA, Hovis KM, Frieman MB, Tran B, Hsia RC, Ravel J, Jenkins-Houk C, Wilson KL, Bavoil PM. SINC, a type III secreted protein of Chlamydia psittaci, targets the inner nuclear membrane of infected cells and uninfected neighbors. Mol Biol Cell 2015; 26:1918-34. [PMID: 25788290 PMCID: PMC4436835 DOI: 10.1091/mbc.e14-11-1530] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/06/2015] [Indexed: 12/31/2022] Open
Abstract
SINC, a new type III secreted protein of the avian and human pathogen Chlamydia psittaci, uniquely targets the nuclear envelope of C. psittaci-infected cells and uninfected neighboring cells. Digitonin-permeabilization studies of SINC-GFP-transfected HeLa cells indicate that SINC targets the inner nuclear membrane. SINC localization at the nuclear envelope was blocked by importazole, confirming SINC import into the nucleus. Candidate partners were identified by proximity to biotin ligase-fused SINC in HEK293 cells and mass spectrometry (BioID). This strategy identified 22 candidates with high confidence, including the nucleoporin ELYS, lamin B1, and four proteins (emerin, MAN1, LAP1, and LBR) of the inner nuclear membrane, suggesting that SINC interacts with host proteins that control nuclear structure, signaling, chromatin organization, and gene silencing. GFP-SINC association with the native LEM-domain protein emerin, a conserved component of nuclear "lamina" structure, or with a complex containing emerin was confirmed by GFP pull down. Our findings identify SINC as a novel bacterial protein that targets the nuclear envelope with the capability of globally altering nuclear envelope functions in the infected host cell and neighboring uninfected cells. These properties may contribute to the aggressive virulence of C. psittaci.
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Affiliation(s)
- Sergio A Mojica
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Kelley M Hovis
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Bao Tran
- Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Ru-ching Hsia
- Core Imaging Facility and Department of Neural and Pain Sciences, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Jacques Ravel
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Clifton Jenkins-Houk
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Patrik M Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
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Abstract
Cell-cell adhesions are necessary for structural integrity and barrier formation of the epidermis. Here, we discuss insights from genetic and cell biological studies into the roles of individual cell-cell junctions and their composite proteins in regulating epidermal development and function. In addition to individual adhesive functions, we will discuss emerging ideas on mechanosensation/transduction of junctions in the epidermis, noncanonical roles for adhesion proteins, and crosstalk/interdependencies between the junctional systems. These studies have revealed that cell adhesion proteins are connected to many aspects of tissue physiology including growth control, differentiation, and inflammation.
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Affiliation(s)
- Kaelyn D Sumigray
- Department of Dermatology, Duke University Medical Center, Durham, North Carolina, USA; Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terry Lechler
- Department of Dermatology, Duke University Medical Center, Durham, North Carolina, USA; Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA.
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78
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Guo Z, Neilson LJ, Zhong H, Murray PS, Zanivan S, Zaidel-Bar R. E-cadherin interactome complexity and robustness resolved by quantitative proteomics. Sci Signal 2014; 7:rs7. [PMID: 25468996 PMCID: PMC4972397 DOI: 10.1126/scisignal.2005473] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
E-cadherin-mediated cell-cell adhesion and signaling plays an essential role in development and maintenance of healthy epithelial tissues. Adhesiveness mediated by E-cadherin is conferred by its extracellular cadherin domains and is regulated by an assembly of intracellular adaptors and enzymes associated with its cytoplasmic tail. We used proximity biotinylation and quantitative proteomics to identify 561 proteins in the vicinity of the cytoplasmic tail of E-cadherin. In addition, we used proteomics to identify proteins associated with E-cadherin-containing adhesion plaques from a cell-glass interface, which enabled the assignment of cellular localization to putative E-cadherin-interacting proteins. Moreover, by tagging identified proteins with GFP (green fluorescent protein), we determined the subcellular localization of 83 putative E-cadherin-proximal proteins and identified 24 proteins that were previously uncharacterized as part of adherens junctions. We constructed and characterized a comprehensive E-cadherin interaction network of 79 published and 394 previously uncharacterized proteins using a structure-informed database of protein-protein interactions. Finally, we found that calcium chelation, which disrupts the interaction of the extracellular E-cadherin domains, did not disrupt most intracellular protein interactions with E-cadherin, suggesting that the E-cadherin intracellular interactome is predominantly independent of cell-cell adhesion.
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Affiliation(s)
- Zhenhuan Guo
- Mechanobiology Institute of Singapore, National University of Singapore, Singapore 117411, Singapore
| | - Lisa J Neilson
- Vascular Proteomics Laboratory, Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Hang Zhong
- Mechanobiology Institute of Singapore, National University of Singapore, Singapore 117411, Singapore
| | - Paul S Murray
- Departments of Biochemistry and Molecular Biophysics and Systems Biology, and Center of Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Sara Zanivan
- Vascular Proteomics Laboratory, Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Ronen Zaidel-Bar
- Mechanobiology Institute of Singapore, National University of Singapore, Singapore 117411, Singapore. Department of Biomedical Engineering, National University of Singapore, Singapore 117575, Singapore.
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79
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Beck DB, Narendra V, Drury WJ, Casey R, Jansen PWTC, Yuan ZF, Garcia BA, Vermeulen M, Bonasio R. In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions. J Proteome Res 2014; 13:6135-43. [PMID: 25311790 PMCID: PMC4261942 DOI: 10.1021/pr500196b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Accurate
and sensitive detection of protein–protein and protein–RNA
interactions is key to understanding their biological functions. Traditional
methods to identify these interactions require cell lysis and biochemical
manipulations that exclude cellular compartments that cannot be solubilized
under mild conditions. Here, we introduce an in vivo proximity labeling
(IPL) technology that employs an affinity tag combined with a photoactivatable
probe to label polypeptides and RNAs in the vicinity of a protein
of interest in vivo. Using quantitative mass spectrometry and deep
sequencing, we show that IPL correctly identifies known protein–protein
and protein–RNA interactions in the nucleus of mammalian cells.
Thus, IPL provides additional temporal and spatial information for
the characterization of biological interactions in vivo.
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Affiliation(s)
- David B Beck
- Howard Hughes Medical Institute and Department of Biochemistry, New York University School of Medicine , 522 First Avenue, New York, New York 10016, United States
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80
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Dingar D, Kalkat M, Chan PK, Srikumar T, Bailey SD, Tu WB, Coyaud E, Ponzielli R, Kolyar M, Jurisica I, Huang A, Lupien M, Penn LZ, Raught B. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors. J Proteomics 2014; 118:95-111. [PMID: 25452129 DOI: 10.1016/j.jprot.2014.09.029] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/23/2014] [Accepted: 09/28/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED The BioID proximity-based biotin labeling technique was recently developed for the characterization of protein-protein interaction networks [1]. To date, this method has been applied to a number of different polypeptides expressed in cultured cells. Here we report the adaptation of BioID to the identification of protein-protein interactions surrounding the c-MYC oncoprotein in human cells grown both under standard culture conditions and in mice as tumor xenografts. Notably, in vivo BioID yielded >100 high confidence MYC interacting proteins, including >30 known binding partners. Putative novel MYC interactors include components of the STAGA/KAT5 and SWI/SNF chromatin remodeling complexes, DNA repair and replication factors, general transcription and elongation factors, and transcriptional co-regulators such as the DNA helicase protein chromodomain 8 (CHD8). Providing additional confidence in these findings, ENCODE ChIP-seq datasets highlight significant coincident binding throughout the genome for the MYC interactors identified here, and we validate the previously unreported MYC-CHD8 interaction using both a yeast two hybrid analysis and the proximity-based ligation assay. In sum, we demonstrate that BioID can be utilized to identify bona fide interacting partners for a chromatin-associated protein in vivo. This technique will allow for a much improved understanding of protein-protein interactions in a previously inaccessible biological setting. BIOLOGICAL SIGNIFICANCE The c-MYC (MYC) oncogene is a transcription factor that plays important roles in cancer initiation and progression. MYC expression is deregulated in more than 50% of human cancers, but the role of this protein in normal cell biology and tumor progression is still not well understood, in part because identifying MYC-interacting proteins has been technically challenging: MYC-containing chromatin-associated complexes are difficult to isolate using traditional affinity purification methods, and the MYC protein is exceptionally labile, with a half-life of only ~30 min. Developing a new strategy to gain insight into MYC-containing protein complexes would thus mark a key advance in cancer research. The recently described BioID proximity-based labeling technique represents a promising new complementary approach for the characterization of protein-protein interactions (PPIs) in cultured cells. Here we report that BioID can also be used to characterize protein-protein interactions for a chromatin-associated protein in tumor xenografts, and present a comprehensive, high confidence in vivo MYC interactome. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
- Dharmendra Dingar
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Manpreet Kalkat
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Swneke D Bailey
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - William B Tu
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Romina Ponzielli
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Max Kolyar
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Annie Huang
- The Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.
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81
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Van Itallie CM, Anderson JM. Architecture of tight junctions and principles of molecular composition. Semin Cell Dev Biol 2014; 36:157-65. [PMID: 25171873 DOI: 10.1016/j.semcdb.2014.08.011] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 08/15/2014] [Accepted: 08/19/2014] [Indexed: 12/11/2022]
Abstract
The tight junction creates an intercellular barrier limiting paracellular movement of solutes and material across epithelia. Currently many proteins have been identified as components of the tight junction and understanding their architectural organization and interactions is critical to understanding the biology of the barrier. In general the architecture can be conceptualized into compartments with the transmembrane barrier proteins (claudins, occludin, JAM-A, etc.), linked to peripheral scaffolding proteins (such as ZO-1, afadin, MAGI1, etc.) which are in turned linked to actin and microtubules through numerous linkers (cingulin, myosins, protein 4.1, etc.). Within this complex network are associated many signaling proteins that affect the barrier and broader cell functions. The PDZ domain is a commonly used motif to specifically link individual junction protein pairs. Here we review some of the key proteins defining the tight junction and general themes of their organization with the perspective that much will be learned about function by characterizing the detailed architecture and subcompartments within the junction.
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Affiliation(s)
- Christina M Van Itallie
- The Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 4525, 50 South Drive, Bethesda, MD 20892, USA.
| | - James M Anderson
- The Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 4525, 50 South Drive, Bethesda, MD 20892, USA.
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82
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Kim DI, Birendra KC, Zhu W, Motamedchaboki K, Doye V, Roux KJ. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc Natl Acad Sci U S A 2014; 111:E2453-61. [PMID: 24927568 PMCID: PMC4066523 DOI: 10.1073/pnas.1406459111] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Proximity-dependent biotin identification (BioID) is a method for identifying protein associations that occur in vivo. By fusing a promiscuous biotin ligase to a protein of interest expressed in living cells, BioID permits the labeling of proximate proteins during a defined labeling period. In this study we used BioID to study the human nuclear pore complex (NPC), one of the largest macromolecular assemblies in eukaryotes. Anchored within the nuclear envelope, NPCs mediate the nucleocytoplasmic trafficking of numerous cellular components. We applied BioID to constituents of the Nup107-160 complex and the Nup93 complex, two conserved NPC subcomplexes. A strikingly different set of NPC constituents was detected depending on the position of these BioID-fusion proteins within the NPC. By applying BioID to several constituents located throughout the extremely stable Nup107-160 subcomplex, we refined our understanding of this highly conserved subcomplex, in part by demonstrating a direct interaction of Nup43 with Nup85. Furthermore, by using the extremely stable Nup107-160 structure as a molecular ruler, we defined the practical labeling radius of BioID. These studies further our understanding of human NPC organization and demonstrate that BioID is a valuable tool for exploring the constituency and organization of large protein assemblies in living cells.
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Affiliation(s)
- Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - K C Birendra
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Wenhong Zhu
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Khatereh Motamedchaboki
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Valérie Doye
- Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France; and
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104;Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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83
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Abstract
Epithelial adhesive cell-to-cell contacts contain large, plasma membrane-spanning multiprotein aggregates that perform vital structural and signaling functions. Three prominent adhesive contacts are the tight junction, adherens junction, and the desmosome. Each junction type has unique cellular functions and a complex molecular composition. In this review, we comment on recent and exciting advances in our understanding of junction composition and function.
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84
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Van Itallie CM, Tietgens AJ, Aponte A, Fredriksson K, Fanning AS, Gucek M, Anderson JM. Biotin ligase tagging identifies proteins proximal to E-cadherin, including lipoma preferred partner, a regulator of epithelial cell-cell and cell-substrate adhesion. J Cell Sci 2013; 127:885-95. [PMID: 24338363 DOI: 10.1242/jcs.140475] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Known proteins associated with the cell-adhesion protein E-cadherin include catenins and proteins involved in signaling, trafficking and actin organization. However, the list of identified adherens junction proteins is likely to be incomplete, limiting investigation into this essential cell structure. To expand the inventory of potentially relevant proteins, we expressed E-cadherin fused to biotin ligase in MDCK epithelial cells, and identified by mass spectrometry neighboring proteins that were biotinylated. The most abundant of the 303 proteins identified were catenins and nearly 40 others that had been previously reported to influence cadherin function. Many others could be rationalized as novel candidates for regulating the adherens junction, cytoskeleton, trafficking or signaling. We further characterized lipoma preferred partner (LPP), which is present at both cell contacts and focal adhesions. Knockdown of LPP demonstrated its requirement for E-cadherin-dependent adhesion and suggested that it plays a role in coordination of the cell-cell and cell-substrate cytoskeletal interactions. The analysis of LPP function demonstrates proof of principle that the proteomic analysis of E-cadherin proximal proteins expands the inventory of components and tools for understanding the function of E-cadherin.
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Affiliation(s)
- Christina M Van Itallie
- Laboratory of Tight Junction Structure and Function, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA
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85
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Abstract
BioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. This technique harnesses a promiscuous biotin ligase to biotinylate proteins based on proximity. The ligase is fused to a protein of interest and expressed in cells, where it biotinylates proximal endogenous proteins. Because it is a rare protein modification in nature, biotinylation of these endogenous proteins by BioID fusion proteins enables their selective isolation and identification with standard biotin-affinity capture. Proteins identified by BioID are candidate interactors for the protein of interest. BioID can be applied to insoluble proteins, can identify weak and/or transient interactions, and is amenable to temporal regulation. Initially applied to mammalian cells, BioID has potential application in a variety of cell types from diverse species.
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Affiliation(s)
- Kyle J Roux
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota
| | - Dae In Kim
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
| | - Brian Burke
- Institute of Medical Biology, Immunos, Singapore
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86
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Sorting nexin 27 (SNX27) associates with zonula occludens-2 (ZO-2) and modulates the epithelial tight junction. Biochem J 2013; 455:95-106. [PMID: 23826934 DOI: 10.1042/bj20121755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins of the SNX (sorting nexin) superfamily are characterized by the presence of a PX (Phox homology) domain and associate with PtdIns3P (phosphatidylinositol-3-monophosphate)-rich regions of the endosomal system. SNX27 is the only sorting nexin that contains a PDZ domain. In the present study, we used a proteomic approach to identify a novel interaction between SNX27 and ZO-2 [zonula occludens-2; also known as TJP2 (tight junction protein 2)], a component of the epithelial tight junction. The SNX27-ZO-2 interaction requires the PDZ domain of SNX27 and the C-terminal PDZ-binding motif of ZO-2. When tight junctions were perturbed by chelation of extracellular Ca2+, ZO-2 transiently localized to SNX27-positive early endosomes. Depletion of SNX27 in mpkCCD (mouse primary kidney cortical collecting duct) cell monolayers resulted in a decrease in the rate of ZO-2, but not ZO-1, mobility at cell-cell contact regions after photobleaching and an increase in junctional permeability to large solutes. The findings of the present study identify an important new SNX27-binding partner and suggest a role for endocytic pathways in the intracellular trafficking of ZO-2 and possibly other tight junction proteins. Our results also indicate a role for SNX27-ZO-2 interactions in tight junction maintenance and function.
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87
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Maiers JL, Peng X, Fanning AS, DeMali KA. ZO-1 recruitment to α-catenin--a novel mechanism for coupling the assembly of tight junctions to adherens junctions. J Cell Sci 2013; 126:3904-15. [PMID: 23813953 DOI: 10.1242/jcs.126565] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The formation of a barrier between epithelial cells is a fundamental determinant of cellular homeostasis, protecting underlying cells against pathogens, dehydration and damage. Assembly of the tight junction barrier is dependent upon neighboring epithelial cells binding to one another and forming adherens junctions, but the mechanism for how these processes are linked is poorly understood. Using a knockdown and substitution system, we studied whether ZO-1 binding to α-catenin is required for coupling tight junction assembly to the formation of adherens junctions. We found that preventing ZO-1 binding to α-catenin did not appear to affect adherens junctions. Rather the assembly and maintenance of the epithelial barrier were disrupted. This disruption was accompanied by alterations in the mobility of ZO-1 and the organization of the actin cytoskeleton. Thus, our study identifies α-catenin binding to ZO-1 as a new mechanism for coupling the assembly of the epithelial barrier to cell-to-cell adhesion.
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Affiliation(s)
- Jessica L Maiers
- The Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA 52242, USA
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88
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Runkle EA, Mu D. Tight junction proteins: from barrier to tumorigenesis. Cancer Lett 2013; 337:41-8. [PMID: 23743355 DOI: 10.1016/j.canlet.2013.05.038] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/16/2013] [Accepted: 05/27/2013] [Indexed: 12/13/2022]
Abstract
The tight junction is a multi-protein complex and is the apical most junctional complex in certain epithelial and endothelial cells. A great deal of attention has been devoted to the understanding of these proteins in contributing to the barrier function - that is, regulating the paracellular flux or permeability between adjacent cells. However, tight junction proteins are now recognized as having functions beyond the barrier. The focus of this review is to discuss the barrier function of the tight junction and to summarize the literature with a focus on the role of tight junction proteins in proliferation, transformation, and metastasis.
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Affiliation(s)
- E Aaron Runkle
- Department of Pathology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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