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Su W, Wang Y, Zou S, Zhao Y, Li Y, Zhang C, Guo X, Li S. Construction of Peptide Library in Mammalian Cells by dsDNA-Based Strategy. ACS OMEGA 2023; 8:1037-1046. [PMID: 36643544 PMCID: PMC9835800 DOI: 10.1021/acsomega.2c06402] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/16/2023]
Abstract
While different display technologies, represented by phage display, have been widely used in drug discovery, they still can hardly achieve function-based peptide screening, which in most cases is performed in mammalian cells. And most attempts to screen functional peptides with mammalian platforms utilized plasmids to store coding information. Our previous work established double-stranded DNAs (dsDNAs) as innovative biological parts to implement AND-gate genetic circuits in mammalian cells. In the current study, we employ dsDNAs with terminal NNK degenerate codons to implement AND-gate genetic circuits and generate peptide libraries in mammalian cells. This dsDNA-based AND-gate (DBAG) peptide library construction strategy is easy to perform, requiring only PCR reaction and cell transfection. High-throughput sequencing (HTS) and single-cell sequencing results revealed both peptide length and amino acid sequence diversity of DBAG peptide libraries. Moreover, as a feasibility test of this strategy, we identified an MDM2-interacting peptide by applying the DBAG peptide library to a mammalian cell-based two-hybrid system. Our work establishes dsDNAs with terminal degenerate codons as biological parts to build peptide libraries in mammalian cells, which may have great application potential in the future.
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Affiliation(s)
- Weijun Su
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Siqi Zou
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yanjie Zhao
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Chunze Zhang
- Department
of Colorectal Surgery, Tianjin Union Medical
Center, Tianjin 300121, China
| | - Xiaojing Guo
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Shuai Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
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2
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Gilda JE, Xu Q, Martinez ME, Nguyen ST, Chase PB, Gomes AV. The functional significance of the last 5 residues of the C-terminus of cardiac troponin I. Arch Biochem Biophys 2016; 601:88-96. [PMID: 26919894 PMCID: PMC4899223 DOI: 10.1016/j.abb.2016.02.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/06/2016] [Accepted: 02/22/2016] [Indexed: 11/15/2022]
Abstract
The C-terminal region of cardiac troponin I (cTnI) is known to be important in cardiac function, as removal of the last 17 C-terminal residues of human cTnI has been associated with myocardial stunning. To investigate the C-terminal region of cTnI, three C-terminal deletion mutations in human cTnI were generated: Δ1 (deletion of residue 210), Δ3 (deletion of residues 208-210), and Δ5 (deletion of residues 206-210). Mammalian two-hybrid studies showed that the interactions between cTnI mutants and cardiac troponin C (cTnC) or cardiac troponin T (cTnT) were impaired in Δ3 and Δ5 mutants when compared to wild-type cTnI. Troponin complexes containing 2-[4'-(iodoacetamido) anilino] naphthalene-6-sulfonic acid (IAANS) labeled cTnC showed that the troponin complex containing cTnI Δ5 had a small increase in Ca(2+) affinity (P < 0.05); while the cTnI Δ1- and Δ3 troponin complexes showed no difference in Ca(2+) affinity when compared to wild-type troponin. In vitro motility assays showed that all truncation mutants had increased Ca(2+) dependent motility relative to wild-type cTnI. These results suggest that the last 5 C-terminal residues of cTnI influence the binding of cTnI with cTnC and cTnT and affect the Ca(2+) dependence of filament sliding, and demonstrate the importance of this region of cTnI.
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Affiliation(s)
- Jennifer E Gilda
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, 95616, USA
| | - Qian Xu
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, 95616, USA
| | - Margaret E Martinez
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Susan T Nguyen
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, 95616, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, 95616, USA.
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Anbarasu K, Sivakumar J. Multidimensional significance of crystallin protein-protein interactions and their implications in various human diseases. Biochim Biophys Acta Gen Subj 2015; 1860:222-33. [PMID: 26365509 DOI: 10.1016/j.bbagen.2015.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Crystallins are the important structural and functional proteins in the eye lens responsible for refractive index. Post-translational modifications (PTMs) and mutations are major causative factors that affect crystallin structural conformation and functional characteristics thus playing a vital role in the etiology of cataractogenesis. SCOPE OF REVIEW The significance of crystallin protein-protein interactions (PPIs) in the lens and non-lenticular tissues is summarized. MAJOR CONCLUSIONS Aberrancy of PPIs between crystallin, its associated protein and metal ions has been accomplished in various human diseases including cataract. A detailed account on multidimensional structural and functional significance of crystallin PPI in humans must be brought into limelight, in order to understand the biochemical and molecular basis augmenting the aberrancies of such interaction. In this scenario, the present review is focused to shed light on studies which will aid to expand our present understanding on disease pathogenesis related to loss of PPI thereby paving the way for putative future therapeutic targets to curb such diseases. GENERAL SIGNIFICANCE The interactions with α-crystallins always aid to protect their structural and functional characteristics. The up-regulation of αB-crystallin in the non-lenticular tissues always decodes as biomarker for various stress related disorders. For better understanding and treatment of various diseases, PPI studies provide overall outline about the structural and functional characteristics of the proteins. This information not only helps to find out the route of cataractogenesis but also aid to identify potential molecules to inhibit/prevent the further development of such complicated phenomenon. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.
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Affiliation(s)
- Kumarasamy Anbarasu
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirapalli 620024, Tamil Nadu, India.
| | - Jeyarajan Sivakumar
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirapalli 620024, Tamil Nadu, India
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4
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Kobayashi T, Suzuki M, Morikawa M, Kino K, Tanuma SI, Miyazawa H. Transcriptional regulation of Tal2 gene by all-trans retinoic acid (atRA) in P19 cells. Biol Pharm Bull 2014; 38:248-56. [PMID: 25482166 DOI: 10.1248/bpb.b14-00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TAL2 is a transcription factor required in the normal development of mouse brain. In a previous study, we demonstrated that the expression of Tal2 gene is induced by the complex of all-trans retinoic acid (atRA) and retinoic acid receptor α (RARα) in mouse embryonal carcinoma P19 cells. atRA is also known to be important in inducing P19 cells to differentiate into the neural lineage. Therefore, we believe that the function of TAL2 in neural differentiation may be clarified by utilizing P19 cells. As the atRA-RARα complex induced the expression of Tal2, we focused on the regulatory region that is involved in its transcription. The atRA-RARα complex occupies a characteristic retinoic acid response element (RARE) located in the promoter of target genes. Therefore, we searched for RARE on the mouse Tal2 and found that a RARE-like element was located in the intron. We also found that a TATA-box-like element was located in the 5'-region of Tal2. Involvement between transcriptional activity and the TATA-box-like element was confirmed in the luciferase assay, and TATA-box binding protein was bound to this element upstream of Tal2 in P19 cells. atRA signaling activated the transcription through the RARE-like element, and RARα was bound to this element on Tal2 in P19 cells. In addition, the interaction between these elements on Tal2 was shown in the chromatin immunoprecipitation assay. These results suggest that the transcription of Tal2 is coordinately mediated by two distal regulatory elements.
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5
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Choi M, Lee S, Choi T, Lee C. A hepatitis C virus NS4B inhibitor suppresses viral genome replication by disrupting NS4B's dimerization/multimerization as well as its interaction with NS5A. Virus Genes 2013; 47:395-407. [PMID: 23868571 DOI: 10.1007/s11262-013-0956-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/08/2013] [Indexed: 01/14/2023]
Abstract
Chronic hepatitis C virus (HCV) infection is responsible for severe liver diseases including liver cirrhosis and hepatocellular carcinoma. An HCV non-structural protein 4B (NS4B) plays an essential role in viral RNA genome replication by building multi-vesicular structures around endoplasmic reticulum membranes. Especially, the second amphipathic helix of NS4B (NS4B-AH2) was shown to be essential for this process. By screening compounds against a membrane-aggregating activity of NS4B-AH2, several anti-HCV replication small molecules targeting NS4B-AH2 were discovered. However, little is known about detailed molecular mechanism of action for these NS4B-AH2 inhibitors. In this report, we provide evidences that NS4B-AH2 is required for NS4B's dimerization/multimerization, its proper subcellular localization, as well as its interaction with NS5A. More importantly, one of NS4B-AH2 inhibitors called "anguizole" was found to be able to disrupt all of these NS4B-AH2-mediated biological functions of NS4B. This newly elucidated mechanism of action will enable us not only to better understand a central role of NS4B-AH2 in HCV life cycle but also to develop a more safe and effective new class of NS4B-AH2 inhibitors of HCV replication in the future.
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Affiliation(s)
- Moonju Choi
- College of Pharmacy, Dongguk University-Seoul, Goyang, 410-050, South Korea
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6
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Lee LY, Wu FH, Hsu CT, Shen SC, Yeh HY, Liao DC, Fang MJ, Liu NT, Yen YC, Dokládal L, Sýkorová E, Gelvin SB, Lin CS. Screening a cDNA library for protein-protein interactions directly in planta. THE PLANT CELL 2012; 24:1746-59. [PMID: 22623495 PMCID: PMC3442567 DOI: 10.1105/tpc.112.097998] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/25/2012] [Accepted: 05/02/2012] [Indexed: 05/18/2023]
Abstract
Screening cDNA libraries for genes encoding proteins that interact with a bait protein is usually performed in yeast. However, subcellular compartmentation and protein modification may differ in yeast and plant cells, resulting in misidentification of protein partners. We used bimolecular fluorescence complementation technology to screen a plant cDNA library against a bait protein directly in plants. As proof of concept, we used the N-terminal fragment of yellow fluorescent protein- or nVenus-tagged Agrobacterium tumefaciens VirE2 and VirD2 proteins and the C-terminal extension (CTE) domain of Arabidopsis thaliana telomerase reverse transcriptase as baits to screen an Arabidopsis cDNA library encoding proteins tagged with the C-terminal fragment of yellow fluorescent protein. A library of colonies representing ~2 × 10(5) cDNAs was arrayed in 384-well plates. DNA was isolated from pools of 10 plates, individual plates, and individual rows and columns of the plates. Sequential screening of subsets of cDNAs in Arabidopsis leaf or tobacco (Nicotiana tabacum) Bright Yellow-2 protoplasts identified single cDNA clones encoding proteins that interact with either, or both, of the Agrobacterium bait proteins, or with CTE. T-DNA insertions in the genes represented by some cDNAs revealed five novel Arabidopsis proteins important for Agrobacterium-mediated plant transformation. We also used this cDNA library to confirm VirE2-interacting proteins in orchid (Phalaenopsis amabilis) flowers. Thus, this technology can be applied to several plant species.
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Affiliation(s)
- Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Chen Shen
- Scientific Instrument Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsuan-Yu Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - De-Chih Liao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Jane Fang
- Core Facilities, Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Nien-Tze Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392
| | - Ladislav Dokládal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanton B. Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Address correspondence to
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7
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KAFI AKM, HATTORI MITSURU, OZAWA TAKEAKI. LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS. ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984410000079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the comparison between fluorescent and bioluminescent proteins, advantages and drawbacks of the bioluminescence techniques are described.
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Affiliation(s)
- A. K. M. KAFI
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - MITSURU HATTORI
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - TAKEAKI OZAWA
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, 3-5 Chiyoda-ku, Tokyo 102-0075, Japan
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8
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Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnol Adv 2011; 29:575-99. [DOI: 10.1016/j.biotechadv.2011.03.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 03/31/2011] [Indexed: 11/24/2022]
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9
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Lee C, Ma H, Hang JQ, Leveque V, Sklan EH, Elazar M, Klumpp K, Glenn JS. The hepatitis C virus NS5A inhibitor (BMS-790052) alters the subcellular localization of the NS5A non-structural viral protein. Virology 2011; 414:10-8. [PMID: 21513964 DOI: 10.1016/j.virol.2011.03.026] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/25/2011] [Accepted: 03/28/2011] [Indexed: 12/31/2022]
Abstract
The hepatitis C virus (HCV) non-structural (NS) 5A protein plays an essential role in the replication of the viral RNA by the membrane-associated replication complex (RC). Recently, a putative NS5A inhibitor, BMS-790052, exhibited the highest potency of any known anti-HCV compound in inhibiting HCV replication in vitro and showed a promising clinical effect in HCV-infected patients. The precise mechanism of action for this new class of potential anti-HCV therapeutics, however, is still unclear. In order to gain further insight into its mode of action, we sought to test the hypothesis that the antiviral effect of BMS-790052 might be mediated by interfering with the functional assembly of the HCV RC. We observed that BMS-790052 indeed altered the subcellular localization and biochemical fractionation of NS5A. Taken together, our data suggest that NS5A inhibitors such as BMS-790052 can suppress viral genome replication by altering the proper localization of NS5A into functional RCs.
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Affiliation(s)
- Choongho Lee
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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Tanaka T, Sewell H, Waters S, Phillips SEV, Rabbitts TH. Single domain intracellular antibodies from diverse libraries: emphasizing dual functions of LMO2 protein interactions using a single VH domain. J Biol Chem 2011; 286:3707-16. [PMID: 20980262 PMCID: PMC3030373 DOI: 10.1074/jbc.m110.188193] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Indexed: 11/06/2022] Open
Abstract
Interfering intracellular antibodies are valuable for biological studies as drug surrogates and as potential macromolecular drugs per se. Their application is still limited because of the difficulty of acquisition of functional intracellular antibodies. We describe the use of the new intracellular antibody capture procedure (IAC(3)) to facilitate direct isolation of functional single domain antibody fragments using four independent target molecules (LMO2, TP53, CRAF1, and Hoxa9) from a set of diverse libraries. Initially, these have variability in only one of the three antigen-binding CDR regions of VH or VL and first round single domains are affinity matured by iterative randomization of the two other CDRs and reselection. We highlight the approach using a single domain binding to LMO2 protein. Our results show that interfering with LMO2 protein function demonstrates a role specifically in erythroid differentiation, confirm a necessary and sufficient function for LMO2 as a cancer therapy target in T-cell neoplasia and allowed for the first time production of soluble recombinant LMO2 protein by co-expression with intracellular domain antibodies. Co-crystallization of LMO2 and the anti-LMO2 VH protein was successful. These results demonstrate that this third generation IAC(3) offers a robust toolbox for various biomedical applications and consolidates functional features of the LMO2 protein complex, which includes the importance of Lmo2-Ldb1 protein interaction.
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Affiliation(s)
- Tomoyuki Tanaka
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Helen Sewell
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Simon Waters
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Simon E. V. Phillips
- Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0FA, United Kingdom
| | - Terence H. Rabbitts
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
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11
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Morrow JS, Rimm DL, Kennedy SP, Cianci CD, Sinard JH, Weed SA. Of Membrane Stability and Mosaics: The Spectrin Cytoskeleton. Compr Physiol 2011. [DOI: 10.1002/cphy.cp140111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Mukherjee S, Mani S. Orphan nuclear receptors as targets for drug development. Pharm Res 2010; 27:1439-68. [PMID: 20372994 PMCID: PMC3518931 DOI: 10.1007/s11095-010-0117-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/04/2010] [Indexed: 12/31/2022]
Abstract
Orphan nuclear receptors regulate diverse biological processes. These important molecules are ligand-activated transcription factors that act as natural sensors for a wide range of steroid hormones and xenobiotic ligands. Because of their importance in regulating various novel signaling pathways, recent research has focused on identifying xenobiotics targeting these receptors for the treatment of multiple human diseases. In this review, we will highlight these receptors in several physiologic and pathophysiologic actions and demonstrate how their functions can be exploited for the successful development of newer drugs.
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Affiliation(s)
- Subhajit Mukherjee
- Departments of Medicine, Genetics and Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 302-D1, Bronx, New York 10461, USA
| | - Sridhar Mani
- Departments of Medicine, Genetics and Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 302-D1, Bronx, New York 10461, USA
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13
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Kim SB, Ozawa T. Creating bioluminescent indicators to visualise biological events in living cells and animals. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.485251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Misawa N, Kafi AKM, Hattori M, Miura K, Masuda K, Ozawa T. Rapid and High-Sensitivity Cell-Based Assays of Protein−Protein Interactions Using Split Click Beetle Luciferase Complementation: An Approach to the Study of G-Protein-Coupled Receptors. Anal Chem 2010; 82:2552-60. [DOI: 10.1021/ac100104q] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naomi Misawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - A. K. M. Kafi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Mitsuru Hattori
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Kenji Miura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Kenji Masuda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
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15
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Waller H, Chatterji U, Gallay P, Parkinson T, Targett-Adams P. The use of AlphaLISA technology to detect interaction between hepatitis C virus-encoded NS5A and cyclophilin A. J Virol Methods 2010; 165:202-10. [PMID: 20132841 DOI: 10.1016/j.jviromet.2010.01.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 01/20/2010] [Accepted: 01/25/2010] [Indexed: 01/27/2023]
Abstract
Cyclosporine A (CsA) is an immunosuppressive molecule that also impedes replication of hepatitis C virus (HCV). CsA inhibits isomerase activity of cellular-encoded cyclophilin proteins, of which cyclophilin A (CypA) in particular is required for HCV replication. Evidence suggests that the HCV-encoded NS5A and NS5B proteins may govern dependence of the virus on CypA-mediated isomerase activity, although the molecular mechanisms involved are unclear. However, association of NS5A and NS5B, with CypA has been reported, raising the possibility that direct interaction between these proteins facilitates HCV replication. In the present study, mammalian two-hybrid and AlphaLISA technologies were utilized to detect interactions between NS5A and NS5B, with CypA. AlphaLISA analysis revealed associations between NS5A and CypA using purified proteins, and in cell lysates prepared from co-transfected cells. Importantly, the NS5A-CypA interactions were sensitive to CsA in a dose-responsive manner and an isomerase mutant of CypA interacted with NS5A less efficiently than wild-type CypA. These findings correlate the anti-HCV properties of CsA with an ability of the compound to disrupt NS5A-CypA interactions in vitro and in vivo, whilst providing the basis for development of assay platforms suitable to screen compound libraries for novel inhibitors of the NS5A-CypA interaction.
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Affiliation(s)
- Helen Waller
- Pfizer Global Research & Development, Antivirals Research Unit (IPC424), Sandwich Laboratories, Sandwich, Kent, CT13 9NJ, UK
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16
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Pan F, Yu H, Dang EV, Barbi J, Pan X, Grosso JF, Jinasena D, Sharma SM, McCadden EM, Getnet D, Drake CG, Liu JO, Ostrowski MC, Pardoll DM. Eos mediates Foxp3-dependent gene silencing in CD4+ regulatory T cells. Science 2009; 325:1142-6. [PMID: 19696312 PMCID: PMC2859703 DOI: 10.1126/science.1176077] [Citation(s) in RCA: 248] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CD4+ regulatory T cells (Tregs) maintain immunological self-tolerance and immune homeostasis by suppressing aberrant or excessive immune responses. The core genetic program of Tregs and their ability to suppress pathologic immune responses depends on the transcription factor Foxp3. Despite progress in understanding mechanisms of Foxp3-dependent gene activation, the molecular mechanism of Foxp3-dependent gene repression remains largely unknown. We identified Eos, a zinc-finger transcription factor of the Ikaros family, as a critical mediator of Foxp3-dependent gene silencing in Tregs. Eos interacts directly with Foxp3 and induces chromatin modifications that result in gene silencing in Tregs. Silencing of Eos in Tregs abrogates their ability to suppress immune responses and endows them with partial effector function, thus demonstrating the critical role that Eos plays in Treg programming.
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Affiliation(s)
- Fan Pan
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Hong Yu
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Eric V. Dang
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Joseph Barbi
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Xiaoyu Pan
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Joseph F. Grosso
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | | | - Sudarshana M. Sharma
- Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210
| | - Erin M. McCadden
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Derese Getnet
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Charles G. Drake
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Jun O. Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Michael C. Ostrowski
- Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210
| | - Drew M. Pardoll
- Immunology and Hematopoiesis Division, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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17
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Umezawa Y. Optical probes for molecular processes in live cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:397-421. [PMID: 20636084 DOI: 10.1146/annurev.anchem.1.031207.112757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this review, I summarize the development over the past several years of fluorescent and/or bioluminescent indicators to pinpoint cellular processes in living cells. These processes involve second messengers, protein phosphorylations, protein-protein interactions, protein-ligand interactions, nuclear receptor-coregulator interactions, nucleocytoplasmic trafficking of functional proteins, and protein localization.
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18
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Kanno A, Ozawa T, Umezawa Y. Intein-mediated reporter gene assay for detecting protein-protein interactions in living mammalian cells. Anal Chem 2007; 78:556-60. [PMID: 16408939 DOI: 10.1021/ac051451a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For nondestructive analysis of chemical processes in living mammalian cells, here we developed a new reporter gene assay for detecting cytosolic protein-protein interactions based on protein splicing of transcription factors with DnaE inteins. The protein splicing induces connection of a DNA-binding protein (modified LexA; mLexA) with a transcription activation domain of a herpes simplex virus protein (VP16AD). We thereby circumvented the limitation of earlier methods for monitoring protein-protein interactions, including the two-hybrid systems, protein complementation systems (PCS), and protein reconstitution systems, and rather combined their advantages. To test the applicability of this method, we monitored epidermal growth factor (EGF)-induced interactions on cell membranes of a known partner, an oncogenic product Ras and its target Raf-1. Ras was connected with N-terminal DnaE and mLexA, while Raf-1 was connected with C-terminal DnaE and VP16AD. Upon stimulation with EGF, the interaction between Ras and Raf-1 triggered folding of the DnaEs, thereby inducing protein splicing to form mLexA-VP16AD fusion protein, and transcription of a reporter gene, firefly luciferase. The extent of Ras-Raf-1 interaction was quantified by measuring the luciferase activity. The interaction was not able to be monitored by two-hybrid systems nor by PCS of split firefly luciferases; however, by using the protein splicing elements and the reporter gene, we obtained the bioluminescence signals sufficient for evaluation of the interactions close to cell membranes.
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Affiliation(s)
- Akira Kanno
- Department of Chemistry, School of Science, The University of Tokyo, Hongo Bunkyo-ku, Tokyo 113-0033, Japan
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19
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Pan F, Sun L, Kardian DB, Whartenby KA, Pardoll DM, Liu JO. Feedback inhibition of calcineurin and Ras by a dual inhibitory protein Carabin. Nature 2007; 445:433-6. [PMID: 17230191 DOI: 10.1038/nature05476] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 11/24/2006] [Indexed: 11/08/2022]
Abstract
Feedback regulation of adaptive immunity is a fundamental mechanism for controlling the overall output of different signal transduction pathways, including that mediated by the T-cell antigen receptor (TCR). Calcineurin and Ras are known to have essential functions during T-cell activation. However, how the calcineurin signalling pathway is terminated in the process is still largely unknown. Although several endogenous inhibitors of calcineurin have been reported, none fulfils the criteria of a feedback inhibitor, as their expression is not responsive to TCR signalling. Here we identify an endogenous inhibitor of calcineurin, named Carabin, which also inhibits the Ras signalling pathway through its intrinsic Ras GTPase-activating protein (GAP) activity. Expression of Carabin is upregulated on TCR signalling in a manner that is sensitive to inhibitors of calcineurin, indicating that Carabin constitutes part of a negative regulatory loop for the intracellular TCR signalling pathway. Knockdown of Carabin by short interfering RNA led to a significant enhancement of interleukin-2 production by antigen-specific T cells in vitro and in vivo. Thus, Carabin is a negative feedback inhibitor of the calcineurin signalling pathway that also mediates crosstalk between calcineurin and Ras.
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Affiliation(s)
- Fan Pan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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20
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21
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Katsu Y, Kohno S, Oka T, Mitsui N, Tooi O, Santo N, Urushitani H, Fukumoto Y, Kuwabara K, Ashikaga K, Minami S, Kato S, Ohta Y, Guillette LJ, Iguchi T. Molecular cloning of estrogen receptor alpha (ERalpha; ESR1) of the Japanese giant salamander, Andrias japonicus. Mol Cell Endocrinol 2006; 257-258:84-94. [PMID: 16919388 DOI: 10.1016/j.mce.2006.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 07/11/2006] [Accepted: 07/13/2006] [Indexed: 11/16/2022]
Abstract
Estrogens are essential for normal reproductive activity in females and males and for ovarian differentiation during a critical developmental stage in many vertebrates. To understand the molecular mechanisms of estrogen action and to evaluate estrogen receptor ligand interactions in the Japanese giant salamander (Andrias japonicus), we isolated cDNA encoding the estrogen receptor (ER) from the liver. A full-length Japanese giant salamander ER cDNA (jgsER) was obtained using 5' and 3' rapid amplification cDNA ends (RACE). The deduced amino acid sequence of the jgsER showed high identity to the Xenopus ERalpha (ESR1) (77.7%). We have applied both the conventional ERE-luciferase reporter assay system and the GAL4-transactivation system to characterize this receptor. In two different transient transfection assay systems using mammalian cells, the jgsER protein displayed estrogen-dependent activation of transcription. The GAL4-transactivation system showed about 10-fold greater activity of the estrogen receptor by hormone when compared to the conventional ERE-luciferase reporter assay system. Tissue distribution of ERalpha mRNA was examined and kidney, ovary and liver exhibited expression. This is the first isolation of an estrogen receptor from a salamander and also is the first functional cDNA obtained from the Japanese giant salamander, an endangered species considered a special natural monument of Japan.
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Affiliation(s)
- Yoshinao Katsu
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
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22
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Oltersdorf T, Elmore SW, Shoemaker AR, Armstrong RC, Augeri DJ, Belli BA, Bruncko M, Deckwerth TL, Dinges J, Hajduk PJ, Joseph MK, Kitada S, Korsmeyer SJ, Kunzer AR, Letai A, Li C, Mitten MJ, Nettesheim DG, Ng S, Nimmer PM, O'Connor JM, Oleksijew A, Petros AM, Reed JC, Shen W, Tahir SK, Thompson CB, Tomaselli KJ, Wang B, Wendt MD, Zhang H, Fesik SW, Rosenberg SH. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 2005; 435:677-81. [PMID: 15902208 DOI: 10.1038/nature03579] [Citation(s) in RCA: 2636] [Impact Index Per Article: 138.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Accepted: 03/31/2005] [Indexed: 12/16/2022]
Abstract
Proteins in the Bcl-2 family are central regulators of programmed cell death, and members that inhibit apoptosis, such as Bcl-X(L) and Bcl-2, are overexpressed in many cancers and contribute to tumour initiation, progression and resistance to therapy. Bcl-X(L) expression correlates with chemo-resistance of tumour cell lines, and reductions in Bcl-2 increase sensitivity to anticancer drugs and enhance in vivo survival. The development of inhibitors of these proteins as potential anti-cancer therapeutics has been previously explored, but obtaining potent small-molecule inhibitors has proved difficult owing to the necessity of targeting a protein-protein interaction. Here, using nuclear magnetic resonance (NMR)-based screening, parallel synthesis and structure-based design, we have discovered ABT-737, a small-molecule inhibitor of the anti-apoptotic proteins Bcl-2, Bcl-X(L) and Bcl-w, with an affinity two to three orders of magnitude more potent than previously reported compounds. Mechanistic studies reveal that ABT-737 does not directly initiate the apoptotic process, but enhances the effects of death signals, displaying synergistic cytotoxicity with chemotherapeutics and radiation. ABT-737 exhibits single-agent-mechanism-based killing of cells from lymphoma and small-cell lung carcinoma lines, as well as primary patient-derived cells, and in animal models, ABT-737 improves survival, causes regression of established tumours, and produces cures in a high percentage of the mice.
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Affiliation(s)
- Tilman Oltersdorf
- Idun Pharmaceuticals, 9380 Judicial Drive, San Diego, California 92121, USA
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23
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Abstract
The interactions between proteins allow the cell's life. A number of experimental, genome-wide, high-throughput studies have been devoted to the determination of protein-protein interactions and the consequent interaction networks. Here, the bioinformatics methods dealing with protein-protein interactions and interaction network are overviewed. 1. Interaction databases developed to collect and annotate this immense amount of data; 2. Automated data mining techniques developed to extract information about interactions from the published literature; 3. Computational methods to assess the experimental results developed as a consequence of the finding that the results of high-throughput methods are rather inaccurate; 4. Exploitation of the information provided by protein interaction networks in order to predict functional features of the proteins; and 5. Prediction of protein-protein interactions.
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Affiliation(s)
- Giacomo Franzot
- International School for Advanced Studies, Via Beirut 4, I-34014 Trieste, Italy
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24
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Hacker HJ, Deres K, Mildenberger M, Schröder CH. Antivirals interacting with hepatitis B virus core protein and core mutations may misdirect capsid assembly in a similar fashion. Biochem Pharmacol 2004; 66:2273-9. [PMID: 14637185 DOI: 10.1016/j.bcp.2003.08.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recently, heteroarylpyrimidines (HAP) have been identified as potent inhibitors of capsid maturation. Here we discuss the HAP mode of action comparing the aggregation phenotype of wild-type and mutant core proteins with the respective phenotype imposed by HAP or other agents interacting with core protein. Pertinent tests include core fusion protein-mediated transactivation in a two-hybrid system and capsid formation. The finding that transactivation appeared to be unaffected by HAP, or by mutations preventing assembly, is surprising and raises the question for the structure of the interacting hybrid core proteins: Are they monomers, dimers or even oligomers? A direct activity of core fusion monomers is not excluded but considered to be highly unlikely due to rapid homodimerisation. A role of core fusion dimers in transactivation would indicate distinct interactions with a differential sensitivity to HAP. Regarding significance of data gained in two-hybrid systems, caution is necessary, since the site of transactivation is the nucleus, whereas the real site of the core protein interactions during replication is the cytoplasm. Apparently, HAP leave the monomer-monomer interface of HBV core protein unaffected but prevent capsid maturation by interacting with a region known to be crucial for dimer multimerisation and formation of stable capsids. It is suggested to use antivirals as tools for the elucidation of early steps in genome replication and capsid assembly. A frame for this could be the hypothesis that the virus uses soluble core protein, namely intracellular maturation intermediates of HbeAg for a core targeted self-restriction of replication.
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Affiliation(s)
- Hans Jörg Hacker
- Department of Virus-Host Interactions (F0600), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
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25
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Chen T, Xie W, Agler M, Banks M. Coactivators in Assay Design for Nuclear Hormone Receptor Drug Discovery. Assay Drug Dev Technol 2003; 1:835-42. [PMID: 15090229 DOI: 10.1089/154065803772613462] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nuclear hormone receptors (NHRs) represent one of the most important drug targets in terms of therapeutic applications. The NHR superfamily consists of a family of DNA binding transcription factors whose function can be controlled by small molecules (steroids or organic acids). Therefore, NHRs are suitable protein targets for the therapies of human diseases. Some of the current marketed drugs, including several anticancer and antidiabetic drugs, are known to target NHRs. Examples include the anticancer and retinoid X receptor-targeting Targretin and the antidiabetic and peroxisome proliferative-activated receptor-gamma-targeting thiaozolidinediones. More NHR-targeting drugs are expected in the coming years. Identification of specific NHR modulators, as well as identification of ligands for orphan NHRs, will lead to new therapies for many human diseases. Many pharmaceutical companies are investing in NHR-targeted drugs, which are estimated to be 10-15% of the US dollars 400 billion global pharmaceutical market. This minireview discusses various aspects of NHR drug discovery, with a focus on the application of NHR coactivators in assay design for NHR ligand identification.
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Affiliation(s)
- Taosheng Chen
- Lead Discovery and Profiling, Bristol-Myers Squibb Company, Wallingford, CT 06492, USA.
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26
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Tanaka T, Lobato MN, Rabbitts TH. Single domain intracellular antibodies: a minimal fragment for direct in vivo selection of antigen-specific intrabodies. J Mol Biol 2003; 331:1109-20. [PMID: 12927545 DOI: 10.1016/s0022-2836(03)00836-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a major need in target validation and therapeutic applications for molecules that can interfere with protein function inside cells. Intracellular antibodies (intrabodies) can bind to specific targets in cells but isolation of intrabodies is currently difficult. Intrabodies are normally single chain Fv fragments comprising variable domains of the immunoglobulin heavy (VH) and light chains (VL). We now demonstrate that single VH domains have excellent intracellular properties of solubility, stability and expression within the cells of higher organisms and can exhibit specific antigen recognition in vivo. We have used this intracellular single variable domain (IDab) format, based on a previously characterised intrabody consensus scaffold, to generate diverse intrabody libraries for direct in vivo screening. IDabs were isolated using two distinct antigens and affinities of isolated IDabs ranged between 20 nM and 200 nM. Moreover, IDabs selected for binding to the RAS protein could inhibit RAS-dependent oncogenic transformation of NIH3T3 cells. The IDab format is therefore ideal for in vivo intrabody use. This approach to intrabodies obviates the need for phage antibody libraries, avoids the requirement for production of antigen in vitro and allows for direct selection of intrabodies in vivo.
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Affiliation(s)
- Tomoyuki Tanaka
- MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK
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27
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Abstract
The availability of complete, annotated genome sequences for a variety of eukaryotic organisms has paved the way for a paradigm shift in biomedical research from the 'one gene-one hypothesis' approach to more global, systematic strategies that analyse genes or proteins on a genome- and proteome-wide scale. One daunting task in the post-genome era is to determine how the complement of expressed cellular proteins - the proteome - is organised into functional, higher-order networks, by mapping all constitutive and dynamic protein-protein interactions. Traditionally, reductionist approaches have typically focused on a few, selected gene products and their interactions in a particular physiological context. In contrast, more holistic strategies aim at understanding complex biological systems, for example global protein-protein interaction networks on a cellular or organismal level. Several large-scale proteomics technologies have been developed to generate comprehensive, cellular protein-protein interaction maps.
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Affiliation(s)
- Gerard Drewes
- Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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28
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Tanaka T, Chung GTY, Forster A, Lobato MN, Rabbitts TH. De novo production of diverse intracellular antibody libraries. Nucleic Acids Res 2003; 31:e23. [PMID: 12595572 PMCID: PMC149845 DOI: 10.1093/nar/gng023] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many therapeutic targets are intracellular proteins and molecules designed to interact with them must effectively bind to their target inside the cell. Intracellular antibodies (intrabodies) recognise and bind to proteins in cells and various methods have been developed to produce such molecules. Intracellular antibody capture (IAC) is based on a genetic screening approach and is a facile methodology with which effective intracellular antibodies can be obtained. During the development of the IAC technology, consensus immunoglobulin variable frameworks were identified which can form the basis of intrabody libraries for direct screening. In this paper, we describe the de novo synthesis of intrabody libraries based on the IAC consensus sequence. The procedure comprises in vitro production of a single antibody gene fragment from oligonucleotides and diversification of CDRs of the immunoglobulin variable domain by mutagenic PCR. Completely de novo intrabody libraries can be rapidly generated in vitro by these approaches. As an example, a single immunoglobulin VH domain intrabody library was screened directly in yeast with an oncogenic BCR-ABL antigen bait and distinct antigen binders were isolated illustrating the functional utility of the library. This second generation IAC approach (IAC2) has many practical advantages, in particular the ability to isolate intrabodies by direct genetic selection, which obviates the need for in vitro production of antigen for pre-selection of antibody fragments.
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Affiliation(s)
- Tomoyuki Tanaka
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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29
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Schmidt MHH, Broll R, Bruch HP, Bögler O, Duchrow M. The proliferation marker pKi-67 organizes the nucleolus during the cell cycle depending on Ran and cyclin B. J Pathol 2003; 199:18-27. [PMID: 12474222 DOI: 10.1002/path.1221] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The proliferation marker pKi-67 ('Ki-67 antigen') is commonly used in clinical and research pathology to detect proliferating cells, as it is only expressed during cell-cycle progression. Despite the fact that this antigen has been known for nearly two decades, there is still no adequate understanding of its function. This study has therefore identified proteins that interact with pKi-67, using a yeast two-hybrid system. A mammalian two-hybrid system and immunoprecipitation studies were used to verify these interactions. Among other cell-cycle regulatory proteins, two binding partners associated with the small GTPase Ran were identified. In addition, DNA-structural and nucleolus-associated proteins binding to pKi-67 were found. Moreover, it was demonstrated that the N-terminal domain of pKi-67 is capable of self-binding to its own repeat region encoded by exon 13. Since RanBP, a protein involved in the transport of macromolecules over the nuclear lamina, was found to be a binding partner, a possible effect of pKi-67 on the localization of cell-cycle regulatory proteins was proposed. To test this hypothesis, a tetracycline-responsive gene expression system was used to induce the pKi-67 fragments previously used for the two-hybrid screens in HeLa cells. Subsequent immunostaining revealed the translocation of cyclin B1 from cytoplasm to nucleoli in response to this expression. It is suggested that pKi-67 is a Ran-associated protein with a role in the disintegration and reformation of the nucleolus and thereby in entry into and exit from the M-phase.
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Affiliation(s)
- M H H Schmidt
- Surgical Research Laboratory, Medical University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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30
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Choi JH, Lee JA, Yim SW, Lim CS, Lee CH, Lee YD, Bartsch D, Kandel ER, Kaang BK. Using an aplysia two-hybrid system to examine the interactions between transcription factors involved in long-term facilitation in the nervous system of aplysia. Learn Mem 2003; 10:40-3. [PMID: 12551962 PMCID: PMC196654 DOI: 10.1101/lm.55303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Interactions between ApCREB1a, ApCREB2, and ApC/EBP have been studied using conventional methods such as the yeast two-hybrid system. However, it is unclear whether these memory-related transcription factors actually interact in the native environment in neurons. To clarify this question, we have developed an Aplysia two-hybrid system and found, consistent with previous studies that ApCREB2 interacts with ApCREB1a and ApC/EBP, and that ApC/EBP forms homodimers. We have also found that ApCREB1a and ApC/EBP do not interact. Therefore, our study shows that formerly described interactions between the proteins actually occur in the Aplysia neurons and that interactions between these transcription factors are specific.
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Affiliation(s)
- Jung-Hwan Choi
- National Research Laboratory, Institute of Molecular Biology and Genetics, School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
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31
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Negro A, Brunati AM, Donella-Deana A, Massimino ML, Pinna LA. Multiple phosphorylation of alpha-synuclein by protein tyrosine kinase Syk prevents eosin-induced aggregation. FASEB J 2002; 16:210-2. [PMID: 11744621 DOI: 10.1096/fj.01-0517fje] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The presence of aggregated alpha-synuclein molecules is a common denominator in a variety of neurodegenerative disorders. Here, we show that alpha-synuclein (alpha-syn) is an outstanding substrate for the protein tyrosine kinase p72syk (Syk), which phosphorylates three tyrosyl residues in its C-terminal domain (Y-125, Y-133, and Y-136), as revealed from experiments with mutants where these residues have been individually or multiply replaced by phenylalanine. In contrast, only Y-125 is phosphorylated by Lyn and c-Fgr. Eosin-induced multimerization is observed with wild-type alpha-syn, either phosphorylated or not by Lyn, and with all its Tyr to Phe mutants but not with the protein previously phosphorylated by Syk. Syk-mediated phosphorylation also counteracts alpha-syn assembly into filaments as judged from the disappearance of alpha-syn precipitated upon centrifugation at 100,000 x g. We also show that Syk and alpha-syn colocalize in the brain, and upon cotransfection in Chinese hamster ovary cells, alpha-syn becomes Tyr-phosphorylated by Syk. Moreover, Syk and alpha-syn interact with each other as judged from the mammalian two-hybrid system approach. These data suggest that Syk or tyrosine kinase(s) with similar specificity may play an antineurodegenerative role by phosphorylating a-syn, thereby preventing its aggregation.
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Affiliation(s)
- Alessandro Negro
- Dipartimento di Chimica Biologica and Centro di Studio delle Biomembrane del C.N.R., University of Padova, Padova, Italy
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32
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Evans DT, Tillman KC, Desrosiers RC. Envelope glycoprotein cytoplasmic domains from diverse lentiviruses interact with the prenylated Rab acceptor. J Virol 2002; 76:327-37. [PMID: 11739697 PMCID: PMC135700 DOI: 10.1128/jvi.76.1.327-337.2002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lentivirus envelope glycoproteins have unusually long cytoplasmic domains compared to those of other retroviruses. To identify cellular binding partners of the simian immunodeficiency virus (SIV) envelope transmembrane protein (gp41) cytoplasmic domain (CD), we performed a yeast two-hybrid screen of a phytohemagglutinin-activated human T-cell cDNA library with the SIV gp41 CD. The majority of positive clones (50 of 54) encoded the prenylated Rab acceptor (PRA1). PRA1 is a 21-kDa protein associated with Golgi membranes that binds to prenylated Rab proteins in their GTP-bound state. While the cellular function of PRA1 is presently unknown, this protein appears to participate in intracellular vesicular trafficking, based on its cellular localization and ability to bind multiple members of the Rab protein family. Mammalian two-hybrid assays confirmed the interaction between the SIV gp41 CD and PRA1. Furthermore, gp41 sequences important for PRA1 binding were mapped to a central leucine-rich, amphipathic alpha-helix in the SIV gp41 cytoplasmic tail. Although the human immunodeficiency virus (HIV-1) gp41 CD failed to interact with PRA1 in the yeast two-hybrid system, its interaction with PRA1 was significantly better than that of the SIV gp41 CD in mammalian two-hybrid assays. Interestingly, PRA1 also interacted with the Env CDs of HIV-2, bovine immunodeficiency virus, equine infectious anemia virus, and feline immunodeficiency virus. Thus, PRA1 associates with envelope glycoproteins from widely divergent lentiviruses.
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Affiliation(s)
- David T Evans
- New England Regional Primate Research Center, Harvard Medical School, Southborough, Massachusetts 01772-9102, USA
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33
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Suzuki H, Fukunishi Y, Kagawa I, Saito R, Oda H, Endo T, Kondo S, Bono H, Okazaki Y, Hayashizaki Y. Protein-protein interaction panel using mouse full-length cDNAs. Genome Res 2001; 11:1758-65. [PMID: 11591653 PMCID: PMC311163 DOI: 10.1101/gr.180101] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed a novel assay system for systematic analysis of protein-protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay system based on the mammalian two-hybrid method. Using gene-specific primers, we successfully constructed the assay samples by two rounds of PCR with up to 3.6 kb from the first-round PCR fragments. In the assay system, we designed all the steps to be performed by adding only samples, reagents, and cells into 384-well assay plates using two types of semiautomatic multiple dispensers. The system enabled us examine more than 20,000 assay wells per day. We detected 145 interactions in our pilot study using 3500 samples derived from mouse full-length enriched cDNAs. Analysis of the interaction data showed both several significant interaction clusters and predicted functions of a few uncharacterized proteins. In combination with our comprehensive mouse full-length cDNA clone bank covering a large part of the whole genes, our high-throughput assay system will discover many interactions to facilitate understanding of the function of uncharacterized proteins and the molecular mechanism of crucial biological processes, and also enable completion of a rough draft of the entire PPI panel in certain cell types or tissues of mouse within a short time.
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Affiliation(s)
- H Suzuki
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
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34
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Golemis EA, Serebriiskii I, Gyuris J, Brent R. Interaction Trap/Two‐Hybrid System to Identify Interacting Proteins. ACTA ACUST UNITED AC 2001; Chapter 4:Unit 4.4. [DOI: 10.1002/0471142301.ns0404s00] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Roger Brent
- Massachusetts General Hospital and Harvard Medical School Boston Massachusetts
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35
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction Trap/Two‐Hybrid System to Identify Interacting Proteins. ACTA ACUST UNITED AC 2001; Chapter 19:Unit19.2. [DOI: 10.1002/0471140864.ps1902s14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - Roger Brent
- The Molecular Sciences Institute Berkeley California
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36
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Golemis EA, Serebriiskii I, Finley RL, Kolonin (hunt by interaction mating MG, Gyuris J, Brent R. Interaction Trap/Two‐Hybrid System to Identify Interacting Proteins. ACTA ACUST UNITED AC 2001; Chapter 20:Unit 20.1. [DOI: 10.1002/0471142727.mb2001s46] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | | | | | - Roger Brent
- The Molecular Sciences Institute Berkeley California
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37
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Jones LC, Whitlock JP. Dioxin-inducible transactivation in a chromosomal setting. Analysis of the acidic domain of the Ah receptor. J Biol Chem 2001; 276:25037-42. [PMID: 11350970 DOI: 10.1074/jbc.m102910200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We analyzed the transactivation function of the acidic segment of the Ah receptor (amino acids 515-583) by reconstituting AhR-defective mouse hepatoma cells with mutants. Our data reveal that both hydrophobic and acidic residues are important for transactivation and that these residues are clustered in two regions of the acidic segment of AhR. Both regions are crucial for function, because disruption of either one substantially impairs transactivation of the chromosomal CYP1A1 target gene. Neither region contains an amino acid motif that resembles those reported for other acidic activation domains. Furthermore, proline substitutions in both regions do not impair transactivation in vivo, a finding that implies that alpha-helix formation is not required for function.
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Affiliation(s)
- L C Jones
- Division of Hematology and Oncology, Cedars Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA 90048, USA
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38
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. CURRENT PROTOCOLS IN CELL BIOLOGY 2001; Chapter 17:Unit 17.3. [PMID: 18228339 PMCID: PMC4095973 DOI: 10.1002/0471143030.cb1703s08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit presents protocols designed to detect interacting proteins. Using yeast as a "test tube" and transcriptional activation of a reporter system, interacting proteins can be identified. The system can also be used to test complex formation for proteins for which there exists a reason to expect interaction.
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Affiliation(s)
- E A Golemis
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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39
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Abstract
Two-hybrid schemes for detecting protein-protein interactions have deepened our understanding of biology by allowing scientists to identify individual important proteins. Recent developments will allow biologists to chart regulatory networks and to rapidly generate hypotheses for the function of genes, allelic variants, and the connections between proteins that make up these networks. Future developments will allow biologists to test inferences about the function of network elements, and allow global approaches to questions of biological function.
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Affiliation(s)
- R Brent
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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40
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Tse E, Rabbitts TH. Intracellular antibody-caspase-mediated cell killing: an approach for application in cancer therapy. Proc Natl Acad Sci U S A 2000; 97:12266-71. [PMID: 11050246 PMCID: PMC17330 DOI: 10.1073/pnas.97.22.12266] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies have been expressed inside cells in an attempt to ablate the function of oncogene products. To make intracellular antibodies more generally applicable and effective in cancer therapy, we have devised a method in which programmed cell death or apoptosis can be triggered by specific antibody-antigen interaction. When intracellular antibodies are linked to caspase 3, the "executioner" in the apoptosis pathway, and bind to the target antigen, the caspase 3 moieties are self-activated and thereby induce cell killing. We have used this strategy in a model system with two pairs of intracellular antibodies and antigens. In vivo coexpression of an antibody-caspase 3 fusion with its antigenic target induced apoptosis that was specific for antibody, antigen, and active caspase 3. Moreover, the antibody-caspase 3 fusion protein was not toxic to cells in the absence of antigen. Therefore, intracellular antibody-mediated apoptosis should be useful as a specific therapeutic approach for the treatment of cancers, a situation where target cell killing is required.
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Affiliation(s)
- E Tse
- Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Hills Road, Cambridge CB2 2QH, United Kingdom
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41
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Shioda T, Andriole S, Yahata T, Isselbacher KJ. A green fluorescent protein-reporter mammalian two-hybrid system with extrachromosomal maintenance of a prey expression plasmid: application to interaction screening. Proc Natl Acad Sci U S A 2000; 97:5220-4. [PMID: 10805780 PMCID: PMC25809 DOI: 10.1073/pnas.97.10.5220] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An improved mammalian two-hybrid system designed for interaction trap screening is described in this paper. CV-1/EBNA-1 monkey kidney epithelial cells expressing Epstein-Barr virus nuclear antigen 1 (EBNA-1) were stably transfected with a reporter plasmid for GAL4-dependent expression of the green fluorescent protein (GFP). A resulting clone, GB133, expressed GFP strongly when transfected transiently with transcriptional activators fused to GAL4 DNA-binding domain with minimal background GFP expression. GB133 cells maintained plasmids containing the OriP Epstein-Barr virus replication origin that directs replication of plasmids in mammalian cells in the presence of the EBNA-1 protein. GB133 cells transfected stably with a model bait expressed GFP when further transfected transiently with an expression plasmid for a known positive prey. When the bait-expressing GB133 cells were transfected transiently with an OriP-containing expression plasmid for the positive prey together with excess amounts of empty vector, cells that received the positive prey were readily identified by green fluorescence in cell culture and eventually formed green fluorescent microcolonies, because the prey plasmid was maintained by the EBNA-1/Ori-P system. The green fluorescent microcolonies were harvested directly from the culture dishes under a fluorescence microscope, and total DNA was then prepared. Prey-encoding cDNA was recovered by PCR using primers annealing to the vector sequences flanking the insert-cloning site. This system should be useful in mammalian cells for efficient screening of cDNA libraries by two-hybrid interaction.
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Affiliation(s)
- T Shioda
- Department of Tumor Biology, The Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.
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42
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Lukac DM, Kirshner JR, Ganem D. Transcriptional activation by the product of open reading frame 50 of Kaposi's sarcoma-associated herpesvirus is required for lytic viral reactivation in B cells. J Virol 1999; 73:9348-61. [PMID: 10516043 PMCID: PMC112969 DOI: 10.1128/jvi.73.11.9348-9361.1999] [Citation(s) in RCA: 322] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is a lymphotropic virus strongly linked to the development of KS, an endothelial cell neoplasm frequent in persons with AIDS. Reactivation from latency in B cells is thought to be an important antecedent to viral spread to endothelial cells during KS pathogenesis. Earlier experiments have posited a role for the transcriptional activator encoded by KSHV open reading frame 50 (ORF50) in such reactivation, since ectopic overexpression of this protein induces reactivation in latently infected B cells. Here we have explored several aspects of the expression, structure, and function of this protein bearing on this role. The ORF50 gene is expressed very early in lytic reactivation, before several other genes implicated as candidate regulatory genes in related viruses, and its expression can upregulate their promoters in transient assays. The protein is extensively phosphorylated in vivo and bears numerous sites for phosphorylation by protein kinase C, activators of which are potent stimulators of lytic induction. The C terminus of the ORF50 protein contains a domain that can strongly activate transcription when targeted to DNA; deletion of this domain generates an allele that expresses a truncated protein which retains the ability to form multimers with full-length ORF50 and functions as a dominant-negative protein. Expression of this allele in latently infected cells ablates spontaneous reactivation from latency and strikingly suppresses viral replication induced by multiple stimuli, including phorbol ester, ionomycin, and sodium butyrate. These results indicate that the ORF50 gene product plays an essential role in KSHV lytic replication and are consistent with its action as a putative molecular switch controlling the induction of virus from latency.
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Affiliation(s)
- D M Lukac
- Department of Microbiology, Howard Hughes Medical Institute, San Francisco, California 94143, USA
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43
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Abstract
Gene reporter systems play a key role in gene expression and regulation studies. This review describes the ideal reporter systems, including reporter expression vector design. It summarizes the many uses of genetic reporters and outlines the currently available and commonly used reporter systems. Each system is described in terms of the reporter gene, the protein it encodes, and the assays available for detecting presence of the reporter. In addition, each reporter system is analyzed in terms of its recommended uses, advantages, and limitations.
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44
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Young KH. A yeast two-hybrid, systems based approach for the identification of novel pharmaceutical entities. Expert Opin Ther Pat 1999. [DOI: 10.1517/13543776.9.7.897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Smith-McCune K, Kalman D, Robbins C, Shivakumar S, Yuschenkoff L, Bishop JM. Intranuclear localization of human papillomavirus 16 E7 during transformation and preferential binding of E7 to the Rb family member p130. Proc Natl Acad Sci U S A 1999; 96:6999-7004. [PMID: 10359828 PMCID: PMC22035 DOI: 10.1073/pnas.96.12.6999] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To study intracellular pathways by which the human papillomavirus 16 oncogene E7 participates in carcinogenesis, we expressed an inducible chimera of E7 by fusion to the hormone-binding domain of the estrogen receptor. The chimeric protein (E7ER) transformed rodent fibroblast cell lines and induced DNA synthesis on addition of estradiol. In coimmunoprecipitation experiments, E7ER preferentially bound p130 when compared to p107 and pRb. After estradiol addition, E7ER localization changed to a more intense intranuclear staining. Induction of E7 function was not correlated with binding to p130 or pRb but rather with intranuclear localization and modest induction of binding to p107.
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Affiliation(s)
- K Smith-McCune
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco CA 94115, USA.
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46
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Tillman K, Oberfield JL, Shen XQ, Bubulya A, Shemshedini L. c-Fos dimerization with c-Jun represses c-Jun enhancement of androgen receptor transactivation. Endocrine 1998; 9:193-200. [PMID: 9867253 DOI: 10.1385/endo:9:2:193] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/1998] [Revised: 06/22/1998] [Accepted: 06/22/1998] [Indexed: 11/11/2022]
Abstract
The transcriptional activity of the human androgen receptor (hAR), like other nuclear receptors, is dependent on accessory factors. One such factor is c-Jun, which has been shown to have a selective function of mediating androgen receptor-dependent transactivation. This c-Jun activity is inhibited by c-Fos, another protooncoprotein that can dimerize with c-Jun to form the transcription factor AP-1. Here we show that c-jun mediates hAR-induced transactivation from the promoter of the androgen-regulated gene, human kallikrein-2 (hKLK2), and c-Fos blocks this activity. Using c-Fos truncation mutants and measuring hKLK2-dependent transcription, we have determined that the bZIP region of c-Fos is required and sufficient for inhibiting c-Jun enhancement of hAR transactivation. Further truncation analysis of the bZIP shows that the c-Fos dimerization function, mediated through the leucine zipper, is essential for the negative activity, whereas DNA binding, mediated through the basic region, is dispensable. These results suggest that heterodimerization by c-Fos with c-Jun blocks c-Jun's ability to enhance hAR-induced transactivation.
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Affiliation(s)
- K Tillman
- University of Toledo, Department of Biology, OH 43606-3390, USA
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47
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Abstract
Two-hybrid technology has contributed significantly to the unraveling of molecular regulatory networks by facilitating the discovery of protein interactions. Outgrowths of these methods are developing rapidly, including interaction mating to identify false positives and map protein networks, two-bait systems, systems not based on transcription, and systems permitting the selection of peptide aptamers to manipulate gene and allele function. These advances promise to have a significant impact on industrial biotechnology and drug development.
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Affiliation(s)
- P Colas
- Laboratoire de Biologie Moléculaire et Cellulaire, UMR49 CNRS/Ecole Normale Supérieure de Lyon, France.
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48
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Schilling B, De-Medina T, Syken J, Vidal M, Münger K. A novel human DnaJ protein, hTid-1, a homolog of the Drosophila tumor suppressor protein Tid56, can interact with the human papillomavirus type 16 E7 oncoprotein. Virology 1998; 247:74-85. [PMID: 9683573 DOI: 10.1006/viro.1998.9220] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have cloned hTid-1, a human homolog of the Drosophila tumor suppressor protein Tid56, by virtue of its ability to form complexes with the human papillomavirus E7 oncoprotein. The carboxyl terminal cysteine-rich metal binding domain of E7 is the major determinant for interaction with hTid-1. The carboxyl terminus of E7 is essential for the functional and structural integrity of E7 and has previously been shown to function as a multimerization domain. The hTid-1 protein is a member of the DnaJ-family of chaperones. Its mRNA is widely expressed in human tissues, including the HPV-18-positive cervical carcinoma cell line HeLa and human genital keratinocytes, the normal host cells of the HPVs. The hTid-1 gene has been mapped to the short arm of chromosome 16. The large tumor antigens of polyomaviruses encode functional J-domains that are important for viral replication as well as cellular transformation. The ability of HPV E7 to interact with a cellular DnaJ protein suggests that these two viral oncoproteins may target common regulatory pathways through J-domains.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 16/genetics
- Cloning, Molecular
- Drosophila/genetics
- Drosophila Proteins
- Female
- Gene Expression
- Genes, Tumor Suppressor
- HSP40 Heat-Shock Proteins
- Heat-Shock Proteins/genetics
- Heat-Shock Proteins/metabolism
- Humans
- Insect Proteins/genetics
- Insect Proteins/metabolism
- Male
- Mitochondrial Proteins
- Molecular Sequence Data
- Oncogene Proteins, Viral/chemistry
- Oncogene Proteins, Viral/genetics
- Oncogene Proteins, Viral/metabolism
- Papillomavirus E7 Proteins
- Pregnancy
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Homology, Amino Acid
- Tissue Distribution
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Affiliation(s)
- B Schilling
- Department of Pathology and Harvard Center for Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Anand G, Yin X, Shahidi AK, Grove L, Prochownik EV. Novel regulation of the helix-loop-helix protein Id1 by S5a, a subunit of the 26 S proteasome. J Biol Chem 1997; 272:19140-51. [PMID: 9235903 DOI: 10.1074/jbc.272.31.19140] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Id proteins negatively regulate the dimerization, DNA binding, and biological properties of basic helix-loop-helix proteins. In a search for novel factors that interact with Id1, we identified a component of the 26 S proteasome, S5a, that has previously been implicated only in the recognition of ubiquitinated polypeptides destined for proteolysis. S5a interacts strongly with Id1, less strongly with the basic helix-loop-helix proteins MyoD and E12, and not at all with other Id proteins. S5a restores DNA binding by MyoD-Id1 and E12-Id1 heterodimers, enhances DNA binding by MyoD and E12 homodimers, and reverses Id1-mediated repression of the muscle creatine kinase promoter during myogenic differentiation. Mutagenesis experiments showed that amino acids flanking the helix-loop-helix domain plus three residues in the first helix of Id1 impart S5a recognition. This requires only the NH2-terminal half of S5a. S5a thus appears to promote the positive regulation of myogenic genes through ubiquitin-independent mechanisms involving inhibition of Id1 and the enhancement of DNA binding by MyoD and E12. This latter property may permit the selection of novel promoter binding sites during myogenesis.
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Affiliation(s)
- G Anand
- Section of Hematology/Oncology, Department of Pediatrics, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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50
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Ko HP, Okino ST, Ma Q, Whitlock JP. Transactivation domains facilitate promoter occupancy for the dioxin-inducible CYP1A1 gene in vivo. Mol Cell Biol 1997; 17:3497-507. [PMID: 9199285 PMCID: PMC232203 DOI: 10.1128/mcb.17.7.3497] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have studied the transcriptional regulation of the dioxin-inducible mouse CYP1A1 gene in its native chromosomal setting. We analyzed the ability of aromatic hydrocarbon receptor (AhR) mutants and AhR chimeras to restore dioxin responsiveness to the CYP1A1 gene in AhR-defective mouse hepatoma cells. Our data reveal that transactivation domains in AhR's C-terminal half mediate occupancy of the nuclear factor 1 site and TATA box for the CYP1A1 promoter in vivo. Transactivation domains of VP16 and AhR nuclear translocator, but not Sp1, can substitute for AhR's C-terminal half in facilitating protein binding at the promoter. Our data also reveal an apparent linear relationship between promoter occupancy and CYP1A1 gene expression in chromatin. These findings provide new insights into the in vivo mechanism of transcriptional activation for an interesting mammalian gene.
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Affiliation(s)
- H P Ko
- Department of Molecular Pharmacology, Stanford University School of Medicine, California 94306-5332, USA
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