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Zhou Y, Wang Y, Zhang D, Liang J. Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses. MOLECULAR PLANT 2024; 17:478-495. [PMID: 38327051 DOI: 10.1016/j.molp.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/28/2023] [Accepted: 02/05/2024] [Indexed: 02/09/2024]
Abstract
ATP-binding cassette (ABC) transporters are integral membrane proteins that have evolved diverse functions fulfilled via the transport of various substrates. In Arabidopsis, the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress responses. In this study, we revealed that two Arabidopsis ABCG transporters, ABCG16 and ABCG25, engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester (ABA-GE), respectively. We first revealed that ABCG16 contributes to osmotic stress tolerance via ABA signaling. More specifically, ABCG16 induces cellular ABA efflux in both yeast and plant cells. Using FRET analysis, we showed that ABCG16 forms obligatory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA, undergoing notable conformational changes. Furthermore, we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum (ER) membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco cells. The specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhibitory role of these two ABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER membrane. Our endomembrane-specific analysis of the FRET signals derived from the homo- or heterodimerized ABCG complexes allowed us to link endomembrane-biased dimerization to the translocation of distinct substrates by ABCG transporters, providing a prototypic framework for understanding the omnipotence of ABCG transporters in plant development and stress responses.
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Affiliation(s)
- Yeling Zhou
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
| | - Yuzhu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Dong Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Jiansheng Liang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
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2
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Zgheib S, Taha N, Zeiger M, Glushonkov O, Lequeu T, Anton H, Didier P, Boutant E, Mély Y, Réal E. The human cellular protein NoL12 is a specific partner of the HIV-1 nucleocapsid protein NCp7. J Virol 2023; 97:e0004023. [PMID: 37695057 PMCID: PMC10537728 DOI: 10.1128/jvi.00040-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/12/2023] [Indexed: 09/12/2023] Open
Abstract
The human immunodeficiency virus-1 (HIV-1) nucleocapsid protein (NCp7) is a nucleic acid chaperone protein with two highly conserved zinc fingers. To exert its key roles in the viral cycle, NCp7 interacts with several host proteins. Among them, the human NoL12 protein (hNoL12) was previously identified in genome wide screens as a potential partner of NCp7. hNoL12 is a highly conserved 25 kDa nucleolar RNA-binding protein implicated in the 5'end processing of ribosomal RNA in the nucleolus and thus in the assembly and maturation of ribosomes. In this work, we confirmed the NCp7/hNoL12 interaction in cells by Förster resonance energy transfer visualized by Fluorescence Lifetime Imaging Microscopy and co-immunoprecipitation. The interaction between NCp7 and hNoL12 was found to strongly depend on their both binding to RNA, as shown by the loss of interaction when the cell lysates were pretreated with RNase. Deletion mutants of hNoL12 were tested for their co-immunoprecipitation with NCp7, leading to the identification of the exonuclease domain of hNoL12 as the binding domain for NCp7. Finally, the interaction with hNoL12 was found to be specific of the mature NCp7 and to require NCp7 basic residues. IMPORTANCE HIV-1 mature nucleocapsid (NCp7) results from the maturation of the Gag precursor in the viral particle and is thus mostly abundant in the first phase of the infection which ends with the genomic viral DNA integration in the cell genome. Most if not all the nucleocapsid partners identified so far are not specific of the mature form. We described here the specific interaction in the nucleolus between NCp7 and the human nucleolar protein 12, a protein implicated in ribosomal RNA maturation and DNA damage response. This interaction takes place in the cell nucleolus, a subcellular compartment where NCp7 accumulates. The absence of binding between hNoL12 and Gag makes hNoL12 one of the few known specific cellular partners of NCp7.
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Affiliation(s)
- Sarwat Zgheib
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Nedal Taha
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Manon Zeiger
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Oleksandr Glushonkov
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Thiebault Lequeu
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Halina Anton
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Pascal Didier
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Emmanuel Boutant
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Yves Mély
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Eléonore Réal
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
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3
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Upstream of N-Ras (Unr/CSDE1) Interacts with NCp7 and Gag, Modulating HIV-1 IRES-Mediated Translation Initiation. Viruses 2022; 14:v14081798. [PMID: 36016420 PMCID: PMC9413769 DOI: 10.3390/v14081798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) nucleocapsid protein (NC) as a mature protein or as a domain of the Gag precursor plays important roles in the early and late phases of the infection. To better understand its roles, we searched for new cellular partners and identified the RNA-binding protein Unr/CSDE1, Upstream of N-ras, whose interaction with Gag and NCp7 was confirmed by co-immunoprecipitation and FRET-FLIM. Unr interaction with Gag was found to be RNA-dependent and mediated by its NC domain. Using a dual luciferase assay, Unr was shown to act as an ITAF (IRES trans-acting factor), increasing the HIV-1 IRES-dependent translation. Point mutations of the HIV-1 IRES in a consensus Unr binding motif were found to alter both the IRES activity and its activation by Unr, suggesting a strong dependence of the IRES on Unr. Interestingly, Unr stimulatory effect is counteracted by NCp7, while Gag increases the Unr-promoted IRES activity, suggesting a differential Unr effect on the early and late phases of viral infection. Finally, knockdown of Unr in HeLa cells leads to a decrease in infection by a non-replicative lentivector, proving its functional implication in the early phase of viral infection.
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Wang J, Jin Y, Li M, Liu S, Lo KKW, Zhao Q. Time-Resolved Luminescent Sensing and Imaging for Enzyme Catalytic Activity Based on Responsive Probes. Chem Asian J 2022; 17:e202200429. [PMID: 35819359 DOI: 10.1002/asia.202200429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Indexed: 11/07/2022]
Abstract
Enzymes, as a kind of biomacromolecules, play an important role in many physiological processes and relate directly to various diseases. Developing an efficient detection method for enzyme activity is important to achieve early diagnosis of enzyme-relevant diseases and high throughput screening of potential enzyme-relevant drugs. Time-resolved luminescence assay provide a high accuracy and signal-to-noise ratios detection methods for enzyme activity, which has been widely used in high throughput screening of enzyme-relevant drugs and diagnosis of enzyme-relevant diseases. Inspired by these advantages, various responsive probes based on metal complexes and metal-free organic compounds have been developed for time-resolved bioimaging and biosensing of enzyme activity owing to their long luminescence lifetimes, high quantum yields and photostability. In this review, we comprehensively reviewed metal complex- and metal-free organic compound-based responsive probes applied to detect enzyme activity through time-resolved imaging, including their design strategies and sensing principles. Current challenges and future prospects in this rapidly growing field are also discussed.
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Affiliation(s)
- Jiawei Wang
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Yibiao Jin
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Mingdang Li
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Shujuan Liu
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Kenneth Kam-Wing Lo
- City University of Hong Kong, Department of Chemistry, Tat Chee Avenue, Hong Kong, CHINA
| | - Qiang Zhao
- Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, 210023, Nanjing, CHINA
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5
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Wang Y, Zhou Y, Liang J. Characterization of Organellar-Specific ABA Responses during Environmental Stresses in Tobacco Cells and Arabidopsis Plants. Cells 2022; 11:2039. [PMID: 35805123 PMCID: PMC9265483 DOI: 10.3390/cells11132039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Abscisic acid (ABA) is a critical phytohormone involved in multifaceted processes in plant metabolism and growth under both stressed and nonstressed conditions. Its accumulation in various tissues and cells has long been established as a biomarker for plant stress responses. To date, a comprehensive understanding of ABA distribution and dynamics at subcellular resolution in response to environmental cues is still lacking. Here, we modified the previously developed ABA sensor ABAleon2.1_Tao3 (Tao3) and targeted it to different organelles including the endoplasmic reticulum (ER), chloroplast/plastid, and nucleus through the addition of corresponding signal peptides. Together with the cytosolic Tao3, we show distinct ABA distribution patterns in different tobacco cells with the chloroplast showing a lower level of ABA in both cell types. In a tobacco mesophyll cell, organellar ABA displayed specific alterations depending on osmotic stimulus, with ABA levels being generally enhanced under a lower and higher concentration of salt and mannitol treatment, respectively. In Arabidopsis roots, cells from both the meristem and elongation zone accumulated ABA considerably in the cytoplasm upon mannitol treatment, while the plastid and nuclear ABA was generally reduced dependent upon specific cell types. In Arabidopsis leaf tissue, subcellular ABA seemed to be less responsive when stressed, with notable increases of ER ABA in epidermal cells and a reduction of nuclear ABA in guard cells. Together, our results present a detailed characterization of stimulus-dependent cell type-specific organellar ABA responses in tobacco and Arabidopsis plants, supporting a highly coordinated regulatory network for mediating subcellular ABA homeostasis during plant adaptation processes.
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Affiliation(s)
- Yuzhu Wang
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China;
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yeling Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiansheng Liang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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6
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Zhou WL, Lin W, Chen Y, Liu Y. Supramolecular assembly confined purely organic room temperature phosphorescence and its biological imaging. Chem Sci 2022; 13:7976-7989. [PMID: 35919429 PMCID: PMC9278158 DOI: 10.1039/d2sc01770a] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Purely organic room temperature phosphorescence, especially in aqueous solution, is attracting increasing attention owing to its large Stokes shift, long lifetime, low preparation cost, low toxicity, good processing performance advantages, and broad application value.
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Affiliation(s)
- Wei-Lei Zhou
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
- College of Chemistry and Material Science, Inner Mongolia Key Laboratory of Chemistry for Nature Products and Synthesis for Functional Molecules, Innovation Team of Optical Functional Molecular Devices, Inner Mongolia Minzu University, Tongliao 028000, P. R. China
| | - Wenjing Lin
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yong Chen
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
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7
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Ahmad T, Ashraf W, Ibrahim A, Zaayter L, Muller CD, Hamiche A, Mély Y, Bronner C, Mousli M. TIP60 governs the auto‑ubiquitination of UHRF1 through USP7 dissociation from the UHRF1/USP7 complex. Int J Oncol 2021; 59:89. [PMID: 34558642 PMCID: PMC8480382 DOI: 10.3892/ijo.2021.5269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Tat interactive protein, 60 kDa (TIP60) is an important partner of ubiquitin-like, containing PHD and RING finger domains 1 (UHRF1), ensuring various cellular processes through its acetyltransferase activity. TIP60 is believed to play a tumor suppressive role, partly explained by its downregulated expression in a number of cancers. The aim of the present study was to investigate the role and mechanisms of action of TIP60 in the regulation of UHRF1 expression. The results revealed that TIP60 overexpression downregulated the UHRF1 and DNA methyltransferase 1 (DNMT1) expression levels. TIP60 interfered with USP7-UHRF1 association and induced the degradation of UHRF1 in an auto-ubiquitination-dependent manner. Moreover, TIP60 activated the p73-mediated apoptotic pathway. Taken together, the data of the present study suggest that the tumor suppressor role of TIP60 is mediated by its regulation to UHRF1.
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Affiliation(s)
- Tanveer Ahmad
- Laboratory of Bioimaging and Pathologies, CNRS UMR‑7021, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch, France
| | - Waseem Ashraf
- Laboratory of Bioimaging and Pathologies, CNRS UMR‑7021, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch, France
| | - Abdulkhaleg Ibrahim
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258 CNRS UMR 7104, University of Strasbourg, 67400 Illkirch, France
| | - Liliyana Zaayter
- Laboratory of Bioimaging and Pathologies, CNRS UMR‑7021, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch, France
| | - Christian D Muller
- Hubert Curien Pluridisciplinary Institute (IPHC), CNRS UMR‑7178, University of Strasbourg, 67401 Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258 CNRS UMR 7104, University of Strasbourg, 67400 Illkirch, France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, CNRS UMR‑7021, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258 CNRS UMR 7104, University of Strasbourg, 67400 Illkirch, France
| | - Marc Mousli
- Laboratory of Bioimaging and Pathologies, CNRS UMR‑7021, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch, France
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8
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Zhou Y, Lu S, Zhi J, Jiang R, Chen J, Zhong H, Shi H, Ma X, An Z. Microscopic Afterglow Bioimaging by Ultralong Organic Phosphorescent Nanoparticles in Living Cells and Zebrafish. Anal Chem 2021; 93:6516-6522. [PMID: 33852275 DOI: 10.1021/acs.analchem.1c00423] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Compared with short-lived emission probes featuring fluorescence imaging , the use of phosphorescent probes imparts the advantage of long-lived signal persistence that distinguishes against background fluorescence interference. However, the realization of ultralong organic phosphorescent (UOP) probes with an ultralong emission lifetime in an aqueous medium is still a challenge. Here, we present a rational strategy for obtaining UOP nanoparticles (NPs) in an air-saturated aqueous medium prepared using an organic phosphor (PDBCz) and a surfactant polymer (PVP), named PDBCz@PVP, showing an ultralong emission lifetime of 284.59 ms and a phosphorescence quantum efficiency of 7.6%. The excellent phosphorescence properties and water solubility of PDBCz@PVP make it a promising candidate for biological imaging. The as-prepared PDBCz@PVP NPs possess excellent luminescence intensity as well as illustrious biocompatibility both in vitro and in vivo. We demonstrate their use as an efficient phosphorescent nanoprobe both in living cells and zebrafish by capturing their afterglow emission signals under microscopy observation for the first time, realizing convenient and fast bioimaging with low cost, which allows for anti-fluorescence interference and shows promise for the future theragnostic applications in nanomedicine.
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Affiliation(s)
- Yudong Zhou
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Song Lu
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Jiahuan Zhi
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Ruihong Jiang
- Sauvage Laboratory for Smart Materials, Shenzhen Bay Laboratory, Harbin Institute of Technology (Shenzhen), No. 9 Duxue Road, Shenzhen 518055, China
| | - Jiahao Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hanbing Zhong
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huifang Shi
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Xing Ma
- Sauvage Laboratory for Smart Materials, Shenzhen Bay Laboratory, Harbin Institute of Technology (Shenzhen), No. 9 Duxue Road, Shenzhen 518055, China
| | - Zhongfu An
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
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9
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Clark NM, Van den Broeck L, Guichard M, Stager A, Tanner HG, Blilou I, Grossmann G, Iyer-Pascuzzi AS, Maizel A, Sparks EE, Sozzani R. Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:789-816. [PMID: 32119794 DOI: 10.1146/annurev-arplant-050718-100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50010, USA;
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
| | - Marjorie Guichard
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Adam Stager
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Ikram Blilou
- Department of Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Guido Grossmann
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
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10
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Zaayter L, Mori M, Ahmad T, Ashraf W, Boudier C, Kilin V, Gavvala K, Richert L, Eiler S, Ruff M, Botta M, Bronner C, Mousli M, Mély Y. A Molecular Tool Targeting the Base-Flipping Activity of Human UHRF1. Chemistry 2019; 25:13363-13375. [PMID: 31322780 DOI: 10.1002/chem.201902605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/18/2019] [Indexed: 12/12/2022]
Abstract
During DNA replication, ubiquitin-like, containing PHD and RING fingers domains 1 (UHRF1) plays key roles in the inheritance of methylation patterns to daughter strands by recognizing through its SET and RING-associated domain (SRA) the methylated CpGs and recruiting DNA methyltransferase 1 (DNMT1). Herein, our goal is to identify UHRF1 inhibitors targeting the 5'-methylcytosine (5mC) binding pocket of the SRA domain to prevent the recognition and flipping of 5mC and determine the molecular and cellular consequences of this inhibition. For this, we used a multidisciplinary strategy combining virtual screening and molecular modeling with biophysical assays in solution and cells. We identified an anthraquinone compound able to bind to the 5mC binding pocket and inhibit the base-flipping process in the low micromolar range. We also showed in cells that this hit impaired the UHRF1/DNMT1 interaction and decreased the overall methylation of DNA, highlighting the critical role of base flipping for DNMT1 recruitment and providing the first proof of concept of the druggability of the 5mC binding pocket. The selected anthraquinone appears thus as a key tool to investigate the role of UHRF1 in the inheritance of methylation patterns, as well as a starting point for hit-to-lead optimizations.
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Affiliation(s)
- Liliyana Zaayter
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Tanveer Ahmad
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Waseem Ashraf
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Vasyl Kilin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Maurizio Botta
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Marc Mousli
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
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11
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Holoubek A, Herman P, Sýkora J, Brodská B, Humpolíčková J, Kráčmarová M, Gášková D, Hof M, Kuželová K. Monitoring of nucleophosmin oligomerization in live cells. Methods Appl Fluoresc 2018; 6:035016. [PMID: 29901450 DOI: 10.1088/2050-6120/aaccb9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oligomerization plays a crucial role in the function of nucleophosmin (NPM), an abundant nucleolar phosphoprotein. Two dual-color methods based on modern fluorescence confocal microscopy are applied for tracking NPM aggregates in live cells: cross-correlation Number and Brightness analysis (ccN&B) combined with pulsed interleaved excitation (PIE) and fluorescence-lifetime imaging microscopy (FLIM) utilizing resonance energy transfer (FRET). HEK-293T cells were transfected with mixture of plasmids designed for tagging with fluorescent proteins so that the cells express mixed population of NPM labeled either with eGFP or mRFP1. We observe joint oligomers formed from the fluorescently labeled NPM. Having validated the in vivo methods, we study an effect of substitutions in cysteine 21 (Cys21) of the NPM N-terminus on the oligomerization to demonstrate applicability of the methods. Inhibitory effect of mutations of the Cys21 to nonpolar Ala or to aromatic Phe on the oligomerization was reported in literature using in vitro semi-native electrophoresis. However, we do not detect any break-up of the joint NPM oligomers due to the Cys21 mutations in live cells. In vivo microscopy observations are supported by an in vitro method, the GFP-Trap immunoprecipitation assay. Our results therefore show importance of utilizing several methods for detection of biologically relevant protein aggregates. In vivo monitoring of the NPM oligomerization, a potential cancer therapy target, by the presented methods offers a new way to monitor effects of drugs that are tested as NPM oligomerization inhibitors directly in live cells.
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Affiliation(s)
- Aleš Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 2094/1, 128 20 Praha 2, Czechia
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12
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Zhang KY, Yu Q, Wei H, Liu S, Zhao Q, Huang W. Long-Lived Emissive Probes for Time-Resolved Photoluminescence Bioimaging and Biosensing. Chem Rev 2018; 118:1770-1839. [DOI: 10.1021/acs.chemrev.7b00425] [Citation(s) in RCA: 479] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kenneth Yin Zhang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Qi Yu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Huanjie Wei
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Shujuan Liu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Qiang Zhao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
- Shaanxi
Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University (NPU), Xi’an 710072, P. R. China
- Key
Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced
Materials (IAM), Jiangsu National Synergetic Innovation Center for
Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing 211800, P. R. China
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13
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Pollpeter D, Parsons M, Sobala AE, Coxhead S, Lang RD, Bruns AM, Papaioannou S, McDonnell JM, Apolonia L, Chowdhury JA, Horvath CM, Malim MH. Deep sequencing of HIV-1 reverse transcripts reveals the multifaceted antiviral functions of APOBEC3G. Nat Microbiol 2018; 3:220-233. [PMID: 29158605 PMCID: PMC6014619 DOI: 10.1038/s41564-017-0063-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022]
Abstract
Following cell entry, the RNA genome of HIV-1 is reverse transcribed into double-stranded DNA that ultimately integrates into the host-cell genome to establish the provirus. These early phases of infection are notably vulnerable to suppression by a collection of cellular antiviral effectors, called restriction or resistance factors. The host antiviral protein APOBEC3G (A3G) antagonizes the early steps of HIV-1 infection through the combined effects of inhibiting viral cDNA production and cytidine-to-uridine-driven hypermutation of this cDNA. In seeking to address the underlying molecular mechanism for inhibited cDNA synthesis, we developed a deep sequencing strategy to characterize nascent reverse transcription products and their precise 3'-termini in HIV-1 infected T cells. Our results demonstrate site- and sequence-independent interference with reverse transcription, which requires the specific interaction of A3G with reverse transcriptase itself. This approach also established, contrary to current ideas, that cellular uracil base excision repair (UBER) enzymes target and cleave A3G-edited uridine-containing viral cDNA. Together, these findings yield further insights into the regulatory interplay between reverse transcriptase, A3G and cellular DNA repair machinery, and identify the suppression of HIV-1 reverse transcriptase by a directly interacting host protein as a new cell-mediated antiviral mechanism.
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Affiliation(s)
- Darja Pollpeter
- Department of Infectious Diseases, King's College London, London, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Andrew E Sobala
- Department of Infectious Diseases, King's College London, London, UK
| | - Sashika Coxhead
- Department of Infectious Diseases, King's College London, London, UK
| | - Rupert D Lang
- Department of Infectious Diseases, King's College London, London, UK
| | - Annie M Bruns
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | - James M McDonnell
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Luis Apolonia
- Department of Infectious Diseases, King's College London, London, UK
| | - Jamil A Chowdhury
- Department of Infectious Diseases, King's College London, London, UK
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, London, UK.
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14
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Abstract
The ligand-regulated structure and biochemistry of nuclear receptor complexes are commonly determined by in vitro studies of isolated receptors, cofactors, and their fragments. However, in the living cell, the complexes that form are governed not just by the relative affinities of isolated cofactors for the receptor but also by the cell-specific sequestration or concentration of subsets of competing or cooperating cofactors, receptors, and other effectors into distinct subcellular domains and/or their temporary diversion into other cellular activities. Most methods developed to understand nuclear receptor function in the cellular environment involve the direct tagging of the nuclear receptor or its cofactors with fluorescent proteins (FPs) and the tracking of those FP-tagged factors by fluorescence microscopy. One of those approaches, Förster resonance energy transfer (FRET) microscopy, quantifies the transfer of energy from a higher energy "donor" FP to a lower energy "acceptor" FP attached to a single protein or to interacting proteins. The amount of FRET is influenced by the ligand-induced changes in the proximities and orientations of the FPs within the tagged nuclear receptor complexes, which is an indicator of the structure of the complexes, and by the kinetics of the interaction between FP-tagged factors. Here, we provide a guide for parsing information about the structure and biochemistry of nuclear receptor complexes from FRET measurements in living cells.
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Affiliation(s)
- Fred Schaufele
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143-0540, USA.
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15
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Anton H, Taha N, Boutant E, Richert L, Khatter H, Klaholz B, Rondé P, Réal E, de Rocquigny H, Mély Y. Investigating the cellular distribution and interactions of HIV-1 nucleocapsid protein by quantitative fluorescence microscopy. PLoS One 2015; 10:e0116921. [PMID: 25723396 PMCID: PMC4344342 DOI: 10.1371/journal.pone.0116921] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 12/12/2022] Open
Abstract
The nucleocapsid protein (NCp7) of the Human immunodeficiency virus type 1 (HIV-1) is a small basic protein containing two zinc fingers. About 2000 NCp7 molecules coat the genomic RNA in the HIV-1 virion. After infection of a target cell, the viral core enters into the cytoplasm, where NCp7 chaperones the reverse transcription of the genomic RNA into the proviral DNA. As a consequence of their much lower affinity for double-stranded DNA as compared to single-stranded RNAs, NCp7 molecules are thought to be released in the cytoplasm and the nucleus of infected cells in the late steps of reverse transcription. Yet, little is known on the cellular distribution of the released NCp7 molecules and on their possible interactions with cell components. Hence, the aim of this study was to identify potential cellular partners of NCp7 and to monitor its intracellular distribution and dynamics by means of confocal fluorescence microscopy, fluorescence lifetime imaging microscopy, fluorescence recovery after photobleaching, fluorescence correlation and cross-correlation spectroscopy, and raster imaging correlation spectroscopy. HeLa cells transfected with eGFP-labeled NCp7 were used as a model system. We found that NCp7-eGFP localizes mainly in the cytoplasm and the nucleoli, where it binds to cellular RNAs, and notably to ribosomal RNAs which are the most abundant. The binding of NCp7 to ribosomes was further substantiated by the intracellular co-diffusion of NCp7 with the ribosomal protein 26, a component of the large ribosomal subunit. Finally, gradient centrifugation experiments demonstrate a direct association of NCp7 with purified 80S ribosomes. Thus, our data suggest that NCp7 molecules released in newly infected cells may primarily bind to ribosomes, where they may exert a new potential role in HIV-1 infection.
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Affiliation(s)
- Halina Anton
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- * E-mail: (YM); (HA)
| | - Nedal Taha
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Emmanuel Boutant
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Heena Khatter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France
| | - Bruno Klaholz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France
| | - Philippe Rondé
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Eléonore Réal
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Hugues de Rocquigny
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- * E-mail: (YM); (HA)
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16
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Role of the nucleocapsid domain in HIV-1 Gag oligomerization and trafficking to the plasma membrane: a fluorescence lifetime imaging microscopy investigation. J Mol Biol 2015; 427:1480-1494. [PMID: 25644662 DOI: 10.1016/j.jmb.2015.01.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 11/20/2022]
Abstract
The Pr55 Gag of human immunodeficiency virus type 1 orchestrates viral particle assembly in producer cells, which requires the genomic RNA and a lipid membrane as scaffolding platforms. The nucleocapsid (NC) domain with its two invariant CCHC zinc fingers flanked by unfolded basic sequences is thought to direct genomic RNA selection, dimerization and packaging during virus assembly. To further investigate the role of NC domain, we analyzed the assembly of Gag with deletions in the NC domain in parallel with that of wild-type Gag using fluorescence lifetime imaging microscopy combined with Förster resonance energy transfer in HeLa cells. We found that, upon binding to nucleic acids, the NC domain promotes the formation of compact Gag oligomers in the cytoplasm. Moreover, the intracellular distribution of the population of oligomers further suggests that oligomers progressively assemble during their trafficking toward the plasma membrane (PM), but with no dramatic changes in their compact arrangement. This ultimately results in the accumulation at the PM of closely packed Gag oligomers that likely arrange in hexameric lattices, as revealed by the perfect match between the experimental Förster resonance energy transfer value and the one calculated from the structural model of Gag in immature viruses. The distal finger and flanking basic sequences, but not the proximal finger, appear to be essential for Gag oligomer compaction and membrane binding. Moreover, the full NC domain was found to be instrumental in the kinetics of Gag oligomerization and intracellular trafficking. These findings further highlight the key roles played by the NC domain in virus assembly.
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17
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Richert L, Didier P, de Rocquigny H, Mély Y. Monitoring HIV-1 Protein Oligomerization by FLIM FRET Microscopy. SPRINGER SERIES IN CHEMICAL PHYSICS 2015. [DOI: 10.1007/978-3-319-14929-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Veeriah S, Leboucher P, de Naurois J, Jethwa N, Nye E, Bunting T, Stone R, Stamp G, Calleja V, Jeffrey SS, Parker PJ, Larijani B. High-throughput time-resolved FRET reveals Akt/PKB activation as a poor prognostic marker in breast cancer. Cancer Res 2014; 74:4983-95. [PMID: 24970478 DOI: 10.1158/0008-5472.can-13-3382] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Dysregulation of the Akt/PKB pathway has been associated with poor prognosis in several human carcinomas. Current approaches to assess Akt activation rely on intensity-based methods, which are limited by the subjectivity of manual scoring and poor specificity. Here, we report the development of a novel assay using amplified, time-resolved Förster resonance energy transfer (FRET), which is highly specific and sensitive and can be adapted to any protein. Using this approach to analyze primary breast tissue microarrays, we quantified levels of activated pAkt at a spatial resolution that revealed molecular heterogeneity within tumors. High pAkt status assessed by amplified FRET correlated with worse disease-free survival. Our findings support the use of amplified FRET to determine pAkt status in cancer tissues as candidate biomarker for the identification of high-risk patients.
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Affiliation(s)
- Selvaraju Veeriah
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Pierre Leboucher
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom. Centre Emotion, Hôpital de la Pitié Salpetriere, Paris, France
| | - Julien de Naurois
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom. Protein Phosphorylation Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Nirmal Jethwa
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Emma Nye
- Experimental Histopathology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Tamara Bunting
- Experimental Histopathology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Richard Stone
- Experimental Histopathology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Gordon Stamp
- Experimental Histopathology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Véronique Calleja
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | | | - Peter J Parker
- Protein Phosphorylation Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom. Cancer Division King's College London, London, United Kingdom
| | - Banafshé Larijani
- Cell Biophysics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom. Cell Biophysics Laboratory, Unidad de Biofísica (CSIC-UPV/EHU), Sarriena s/n, Leioa, Spain. Ikerbasque, Basque Foundation for Science, University of the Basque Country, Sarriena s/n, Leioa, Spain.
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19
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Role of the nucleocapsid region in HIV-1 Gag assembly as investigated by quantitative fluorescence-based microscopy. Virus Res 2014; 193:78-88. [PMID: 25016037 DOI: 10.1016/j.virusres.2014.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 06/17/2014] [Accepted: 06/17/2014] [Indexed: 11/19/2022]
Abstract
The Gag precursor of HIV-1, formed of the four proteic regions matrix (MA), capsid (CA), nucleocapsid (NC) and p6, orchestrates virus morphogenesis. This complex process relies on three major interactions, NC-RNA acting as a scaffold, CA-CA and MA-membrane that targets assembly to the plasma membrane (PM). The characterization of the molecular mechanism of retroviral assembly has extensively benefited from biochemical studies and more recently an important step forward was achieved with the use of fluorescence-based techniques and fluorescently labeled viral proteins. In this review, we summarize the findings obtained with such techniques, notably quantitative-based approaches, which highlight the role of the NC region in Gag assembly.
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20
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Tavares E, Macedo JA, Paulo PM, Tavares C, Lopes C, Melo EP. Live-cell FRET imaging reveals clustering of the prion protein at the cell surface induced by infectious prions. Biochim Biophys Acta Mol Basis Dis 2014; 1842:981-91. [DOI: 10.1016/j.bbadis.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 01/16/2023]
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21
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Holmes-Smith AS, Hollas AC, McLoskey D, Hungerford G. Viability of Saccharomyces cerevisiae incorporated within silica and polysaccharide hosts monitored via time-resolved fluorescence. Photochem Photobiol Sci 2013; 12:2186-94. [PMID: 24145860 DOI: 10.1039/c3pp50202c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The viability of Saccharomyces cerevisiae in biocompatible polymers under different growth conditions and studied using time-resolved fluorescence techniques is presented. Two fluorophores, the viscosity sensitive probe 4-(4-(dimethylamino)styryl)-N-methyl-pyridiniumiodine (DASPMI) and the yeast viability stain 2-chloro-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene)-1-phenylquinolinium iodide (FUN-1) are used to elucidate information on the incorporated yeast cell viability. Variations in cell viscosity, which are indicative of the cell state, were obtained using DASPMI. Prior to observing FUN-1 in yeast cells using fluorescence lifetime imaging, its photophysics in solution and heterogeneous media were investigated. Time-resolved emission spectra were measured and analysed to associate lifetimes to the spectral emission. Preliminary results show that monitoring the fluorescence lifetime of FUN-1 may give a useful insight into cellular metabolism. The results indicate that both fluorophores may be used to monitor the entrapped yeast cell viability, which is important for in vitro studies and applications, such as that in the biofuel industry, where Saccharomyces cerevisiae are required to remain active in high ethanol environments.
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Affiliation(s)
- A Sheila Holmes-Smith
- School of Engineering and Built Environment, Glasgow Caledonian University, Cowcaddens Road, Glasgow, G4 0BA, UK.
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22
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Mergenthaler P, Wendland K, Meisel A. A versatile tool for the analysis of neuronal survival. Methods 2013; 66:325-9. [PMID: 23981362 DOI: 10.1016/j.ymeth.2013.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/31/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
To understand the principles that govern mechanisms of neuronal survival or death it is necessary to systematically model these processes. Methods involving overexpression or knockdown of a gene of interest using non-viral transfection of primary neurons can easily be adapted to study cell death pathways in primary neurons. However, common biochemical approaches to measure cell death are insufficient to measure neuronal viability in these systems. To investigate the functional role of genes in cultured neurons, we therefore established a cell-based assay using a cotransfection/cocultivation approach in primary cortical neurons from mouse or rat. Using this method, it is possible to use well-established cell culture models of neuronal damage, and to analyze cell survival in genetically different neurons on a single-cell basis following apoptotic stimuli under identical conditions. The duration of the entire protocol is 10 days. Finally, the method may be applicable to a wide range of damage models, primary cells, and cell lines as well as it can be used for high content screening (HCS) studies and downstream image cytometry.
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Affiliation(s)
- Philipp Mergenthaler
- Department of Experimental Neurology, Department of Neurology, Center for Stroke Research, NeuroCure Cluster of Excellence, Charité University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Kristin Wendland
- Department of Experimental Neurology, Department of Neurology, Center for Stroke Research, NeuroCure Cluster of Excellence, Charité University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Andreas Meisel
- Department of Experimental Neurology, Department of Neurology, Center for Stroke Research, NeuroCure Cluster of Excellence, Charité University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
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23
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Abstract
The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G [A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and the nucleocapsid domain of Pr55(Gag). Recently, we showed that oligomerization of Vif into high-molecular-mass complexes induces Vif folding and influences its binding to high-affinity RNA binding sites present in the HIV genomic RNA. To get further insight into the role of Vif multimerization in viral assembly and A3G repression, we used fluorescence lifetime imaging microscopy (FLIM)- and fluorescence resonance energy transfer (FRET)-based assays to investigate Vif-Vif interactions in living cells. By using two N-terminally tagged Vif proteins, we show that Vif-Vif interactions occur in living cells. This oligomerization is strongly reduced when the putative Vif multimerization domain ((161)PPLP(164)) is mutated, indicating that this domain is crucial, but that regions outside this motif also participate in Vif oligomerization. When coexpressed together with Pr55(Gag), Vif is largely relocated to the cell membrane, where Vif oligomerization also occurs. Interestingly, wild-type A3G strongly interferes with Vif multimerization, contrary to an A3G mutant that does not bind to Vif. These findings confirm that Vif oligomerization occurs in living cells partly through its C-terminal motif and suggest that A3G may target and perturb the Vif oligomerization state to limit its functions in the cell.
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24
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Rinaldi AS, Freund G, Desplancq D, Sibler AP, Baltzinger M, Rochel N, Mély Y, Didier P, Weiss E. The use of fluorescent intrabodies to detect endogenous gankyrin in living cancer cells. Exp Cell Res 2013; 319:838-49. [PMID: 23353833 DOI: 10.1016/j.yexcr.2013.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/07/2012] [Accepted: 01/10/2013] [Indexed: 01/31/2023]
Abstract
Expression of antibody fragments in mammalian cells (intrabodies) is used to probe the target protein or interfere with its biological function. We previously described the in vitro characterisation of a single-chain Fv (scFv) antibody fragment (F5) isolated from an intrabody library that binds to the oncoprotein gankyrin (GK) in solution. Here, we have isolated several other scFvs that interact with GK in the presence of F5 and tested whether they allow, when fused to fluorescent proteins, to detect by FRET endogenous GK in living cells. The binding of pairs of scFvs to GK was analysed by gel filtration and the ability of each scFv to mediate nuclear import/export of GK was determined. Binding between scFv-EGFP and RFP-labelled GK in living cells was detected by fluorescence lifetime imaging microscopy (FLIM). After co-transfection of two scFvs fused to EGFP and RFP, respectively, which form a tri-molecular complex with GK in vitro, FRET signal was measured. This system allowed us to observe that GK is monomeric and distributed throughout the cytoplasm and nucleus of several cancer cell lines. Our results show that pairs of fluorescently labelled intrabodies can be monitored by FLIM-FRET microscopy and that this technique allows the detection of lowly expressed endogenous proteins in single living cells.
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Affiliation(s)
- Anne-Sophie Rinaldi
- Ecole Supérieure de Biotechnologie de Strasbourg, UMR 7242, CNRS/Université de Strasbourg, boulevard Sébastien Brant, 67412 Illkirch, France
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25
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DNA-dependent Oct4-Sox2 interaction and diffusion properties characteristic of the pluripotent cell state revealed by fluorescence spectroscopy. Biochem J 2013; 448:21-33. [PMID: 22909387 DOI: 10.1042/bj20120725] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Oct4 and Sox2 are two essential transcription factors that co-regulate target genes for the maintenance of pluripotency. However, it is unclear whether they interact prior to DNA binding or how the target sites are accessed in the nucleus. By generating fluorescent protein fusions of Oct4 and Sox2 that are functionally capable of producing iPSCs (induced pluripotent stem cells), we show that their interaction is dependent on the presence of cognate DNA-binding elements, based on diffusion time, complex formation and lifetime measurements. Through fluorescence correlation spectroscopy, the levels of Oct4 and Sox2 in the iPSCs were quantified in live cells and two diffusion coefficients, corresponding to free and loosely bound forms of the protein, were distinguished. Notably, the fraction of slow-diffusing molecules in the iPSCs was found to be elevated, similar to the profile in embryonic stem cells, probably due to a change in the nuclear milieu during reprogramming. Taken together, these findings have defined quantitatively the amount of proteins pertinent to the pluripotent state and revealed increased accessibility to the underlying DNA as a mechanism for Oct4 and Sox2 to find their target binding sites and interact, without prior formation of heterodimer complexes.
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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Desmond CR, Atwal RS, Xia J, Truant R. Identification of a karyopherin β1/β2 proline-tyrosine nuclear localization signal in huntingtin protein. J Biol Chem 2012; 287:39626-33. [PMID: 23012356 DOI: 10.1074/jbc.m112.412379] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Among the known pathways of protein nuclear import, the karyopherin β2/transportin pathway is only the second to have a defined nuclear localization signal (NLS) consensus. Huntingtin, a 350-kDa protein, has defined roles in the nucleus, as well as a CRM1/exportin-dependent nuclear export signal; however, the NLS and exact pathway of import have remained elusive. Here, using a live cell assay and affinity chromatography, we show that huntingtin has a karyopherin β2-dependent proline-tyrosine (PY)-NLS in the amino terminus of the protein. This NLS comprises three consensus components: a basic charged sequence, a downstream conserved arginine, and a PY sequence. Unlike the classic PY-NLS, which has an unstructured intervening sequence between the consensus components, we show that a β sheet structured region separating the consensus elements is critical for huntingtin NLS function. The huntingtin PY-NLS is also capable of import through the importin/karyopherin β1 pathway but was not functional in all cell types tested. We propose that this huntingtin PY-NLS may comprise a new class of multiple import factor-dependent NLSs with an internal structural component that may regulate NLS activity.
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Affiliation(s)
- Carly R Desmond
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N3Z5
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Abstract
The androgen receptor (AR) is the central component of a dynamic conformational and interaction cascade initiated by androgenic hormones. AR function can be modified by cellular inputs not examined in test tube studies of AR action. Thus, there is a need to measure AR conformation and biochemistry directly within the cell where the intracellular locations, levels and availability of the hormone, AR, AR-interacting factors, DNA-binding sites, enzymes that modify those components of AR action, and factors that compete for the formation of functional AR-cofactor complexes may affect AR action. The dynamic nature of the AR functional cycle itself may introduce temporal fluctuations in factor status and location to affect AR output in the intact cell. This chapter focuses on the method of Förster resonance energy transfer which uniquely has the resolving power and ability to directly measure the conformation and biochemistry of AR signaling in living cells.
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Hayakawa EH, Furutani M, Matsuoka R, Takakuwa Y. Comparison of protein behavior between wild-type and G601S hERG in living cells by fluorescence correlation spectroscopy. J Physiol Sci 2011; 61:313-9. [PMID: 21573751 PMCID: PMC10717380 DOI: 10.1007/s12576-011-0150-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/17/2011] [Indexed: 11/24/2022]
Abstract
The human ether-a-go-go-related gene (hERG) protein is a cardiac potassium channel. Mutations in hERG can result in reductions in membrane channel current, cardiac repolarization, prolongation of QT intervals, and lethal arrhythmia. In the last decade, it has been found that some mutants of hERG involved in long QT syndrome exhibit intracellular protein trafficking defects, while other mutants sort to the membrane but cannot form functional channels. Due to the close relationship between intracellular trafficking and functional protein expression, we aimed to measure differences in protein behavior/motion between wild-type and mutant hERG by directly analyzing the fluorescence fluctuations of green fluorescent protein-labeled proteins using fluorescence correlation spectroscopy (FCS). Our data imply that FCS can be applied as a new diagnostic tool to assess whether the defect in a particular mutant channel protein involves aberrant intracellular trafficking.
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Affiliation(s)
- Eri H. Hayakawa
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Present Address: Laboratory of Medical Zoology and Parasitology, Department of Infection and Immunity, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Michiko Furutani
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Pediatric Cardiology, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Rumiko Matsuoka
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Pediatric Cardiology, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Yuichi Takakuwa
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Biochemistry, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
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Alanine zipper-like coiled-coil domains are necessary for homotypic dimerization of plant GAGA-factors in the nucleus and nucleolus. PLoS One 2011; 6:e16070. [PMID: 21347358 PMCID: PMC3037368 DOI: 10.1371/journal.pone.0016070] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 12/06/2010] [Indexed: 01/09/2023] Open
Abstract
GAGA-motif binding proteins control transcriptional activation or repression of homeotic genes. Interestingly, there are no sequence similarities between animal and plant proteins. Plant BBR/BPC-proteins can be classified into two distinct groups: Previous studies have elaborated on group I members only and so little is known about group II proteins. Here, we focused on the initial characterization of AtBPC6, a group II protein from Arabidopsis thaliana. Comparison of orthologous BBR/BPC sequences disclosed two conserved signatures besides the DNA binding domain. A first peptide signature is essential and sufficient to target AtBPC6-GFP to the nucleus and nucleolus. A second domain is predicted to form a zipper-like coiled-coil structure. This novel type of domain is similar to Leucine zippers, but contains invariant alanine residues with a heptad spacing of 7 amino acids. By yeast-2-hybrid and BiFC-assays we could show that this Alanine zipper domain is essential for homotypic dimerization of group II proteins in vivo. Interhelical salt bridges and charge-stabilized hydrogen bonds between acidic and basic residues of the two monomers are predicted to form an interaction domain, which does not follow the classical knobs-into-holes zipper model. FRET-FLIM analysis of GFP/RFP-hybrid fusion proteins validates the formation of parallel dimers in planta. Sequence comparison uncovered that this type of domain is not restricted to BBR/BPC proteins, but is found in all kingdoms.
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Abstract
Imaging cytometry has recently become an important achievement in development of flow cytometric technologies. The ImageStream cytometer combines the vast features of classical flow cytometry including an impartial analysis of great number of cells in short period of time which results in strong statistical data output, with essential features of fluorescence microscopy such us collecting of real multiparameter images of analyzed objects. In this chapter, we would like to introduce an overview of imaging cytometry platform and emphasize the potential advantages of using this system for several experimental purposes. Moreover, both well established as well as potential applications of imaging cytometry will be described. Eventually, we would like to illustrate the unique use of ImageStream cytometer for identification and characterization of subpopulations of stem/ progenitor cells present in different biological specimens.
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Affiliation(s)
- Ewa K Zuba-Surma
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Sánchez-Álvarez M, Sánchez-Hernández N, Suñé C. Spatial Organization and Dynamics of Transcription Elongation and Pre-mRNA Processing in Live Cells. GENETICS RESEARCH INTERNATIONAL 2011; 2011:626081. [PMID: 22567362 PMCID: PMC3335512 DOI: 10.4061/2011/626081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
During the last 30 years, systematic biochemical and functional studies have significantly expanded our knowledge of the transcriptional molecular components and the pre-mRNA processing machinery of the cell. However, our current understanding of how these functions take place spatiotemporally within the highly compartmentalized eukaryotic nucleus remains limited. Moreover, it is increasingly clear that “the whole is more than the sum of its parts” and that an understanding of the dynamic coregulation of genes is essential for fully characterizing complex biological phenomena and underlying diseases. Recent technological advances in light microscopy in addition to novel cell and molecular biology approaches have led to the development of new tools, which are being used to address these questions and may contribute to achieving an integrated and global understanding of how the genome works at a cellular level. Here, we review major hallmarks and novel insights in RNA polymerase II activity and pre-mRNA processing in the context of nuclear organization, as well as new concepts and challenges arising from our ability to gather extensive dynamic information at the single-cell resolution.
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Affiliation(s)
- Miguel Sánchez-Álvarez
- Dynamical Cell Systems Team, Section of Cellular and Molecular Biology, The Institute of Cancer Research, London SW3 6JB, UK
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33
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Strohhöfer C, Förster T, Chorvát D, Kasák P, Lacík I, Koukaki M, Karamanou S, Economou A. Quantitative analysis of energy transfer between fluorescent proteins in CFP–GBP–YFP and its response to Ca2+. Phys Chem Chem Phys 2011; 13:17852-63. [DOI: 10.1039/c1cp21088b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Barber PR, Ameer-Beg SM, Pathmananthan S, Rowley M, Coolen ACC. A Bayesian method for single molecule, fluorescence burst analysis. BIOMEDICAL OPTICS EXPRESS 2010; 1:1148-1158. [PMID: 21258537 PMCID: PMC3018088 DOI: 10.1364/boe.1.001148] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 10/04/2010] [Indexed: 05/18/2023]
Abstract
There is currently great interest in determining physical parameters, e.g. fluorescence lifetime, of individual molecules that inform on environmental conditions, whilst avoiding the artefacts of ensemble averaging. Protein interactions, molecular dynamics and sub-species can all be studied. In a burst integrated fluorescence lifetime (BIFL) experiment, identification of fluorescent bursts from single molecules above background detection is a problem. This paper presents a Bayesian method for burst identification based on model selection and demonstrates the detection of bursts consisting of 10% signal amplitude. The method also estimates the fluorescence lifetime (and its error) from the burst data.
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Affiliation(s)
- P. R. Barber
- University of Oxford, Gray Institute for Radiation Oncology and Biology,
Old Road Campus, Oxford OX3 7DQ, UK
- King's College London, Division of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research,
Guy's Campus, London SE1 1UL, UK
| | - S. M. Ameer-Beg
- King's College London, Division of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research,
Guy's Campus, London SE1 1UL, UK
| | - S. Pathmananthan
- King's College London, Division of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research,
Guy's Campus, London SE1 1UL, UK
| | - M. Rowley
- King's College London, Division of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research,
Guy's Campus, London SE1 1UL, UK
| | - A. C. C. Coolen
- King's College London, Division of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research,
Guy's Campus, London SE1 1UL, UK
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36
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Affiliation(s)
- Mikhail Y. Berezin
- Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, USA, Tel. 314-747-0701, 314-362-8599, fax 314-747-5191
| | - Samuel Achilefu
- Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, USA, Tel. 314-747-0701, 314-362-8599, fax 314-747-5191
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HIV-1 Vpr oligomerization but not that of Gag directs the interaction between Vpr and Gag. J Virol 2009; 84:1585-96. [PMID: 19923179 DOI: 10.1128/jvi.01691-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During HIV-1 assembly, the viral protein R (Vpr) is incorporated into newly made viral particles via an interaction with the C-terminal domain of the Gag polyprotein precursor Pr55(Gag). Vpr has been implicated in the nuclear import of newly made viral DNA and subsequently in its transcription. In addition, Vpr can affect the cell physiology by causing G(2)/M cell cycle arrest and apoptosis. Vpr can form oligomers, but their roles have not yet been investigated. We have developed fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer-based assays to monitor the interaction between Pr55(Gag) and Vpr in HeLa cells. To that end, we used enhanced green fluorescent protein-Vpr that can be incorporated into the virus and tetracysteine (TC)-tagged Pr55(Gag)-TC. This TC motif is tethered to the C terminus of Pr55(Gag) and does not interfere with Pr55(Gag) trafficking and the assembly of virus-like particles (VLPs). Results show that the Pr55(Gag)-Vpr complexes accumulated mainly at the plasma membrane. In addition, results with Pr55(Gag)-TC mutants confirm that the (41)LXXLF domain of Gag-p6 is essential for Pr55(Gag)-Vpr interaction. We also report that Vpr oligomerization is crucial for Pr55(Gag) recognition and its accumulation at the plasma membrane. On the other hand, Pr55(Gag)-Vpr complexes are still formed when Pr55(Gag) carries mutations impairing its multimerization. These findings suggest that Pr55(Gag)-Vpr recognition and complex formation occur early during Pr55(Gag) assembly.
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38
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Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1. Amino Acids 2009; 38:1583-93. [DOI: 10.1007/s00726-009-0378-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 10/14/2009] [Indexed: 10/20/2022]
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39
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Blanco AM, Rausell L, Aguado B, Perez-Alonso M, Artero R. A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization. Nucleic Acids Res 2009; 37:e116. [PMID: 19561195 PMCID: PMC2761257 DOI: 10.1093/nar/gkp551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We describe a quantitative method for detecting RNA alternative splicing variants that combines in situ hybridization of fluorescently labeled peptide nucleic acid (PNA) probes with confocal microscopy Förster resonance energy transfer (FRET). The use of PNA probes complementary to sequences flanking a given splice junction allows to specifically quantify, within the cell, the RNA isoform generating such splice junction by FRET measure. As a proof of concept we analyzed two alternative splicing events originating from lymphocyte antigen 6 (LY6) complex, locus G5B (LY6G5B) pre-mRNA. These are characterized by the removal of the first intron (Fully Spliced Isoform, FSI) or by retention of such intron (Intron-Retained Isoform, IRI). The use of PNA probe pairs labeled with donor (Cy3) and acceptor (Cy5) fluorophores, suitable to FRET, flanking FSI and IRI specific splice junctions specifically detected both mRNA isoforms in HeLa cells. We have observed that the method works efficiently with probes 5–11 nt apart. The data supports that this FRET-based PNA fluorescence in situ hybridization (FP–FISH) method offers a conceptually new approach for characterizing at the subcellular level not only splice variant isoform structure, location and dynamics but also potentially a wide variety of close range RNA–RNA interactions.
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Affiliation(s)
- Ana M Blanco
- Sistemas Genómicos S.L., Parque Tecnológico de Valencia, Ronda G. Marconi 6, E-46980 Paterna, Spain
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Barber P, Ameer-Beg S, Gilbey J, Carlin L, Keppler M, Ng T, Vojnovic B. Multiphoton time-domain fluorescence lifetime imaging microscopy: practical application to protein–protein interactions using global analysis. J R Soc Interface 2008. [DOI: 10.1098/rsif.2008.0451.focus] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Förster resonance energy transfer (FRET) detected via fluorescence lifetime imaging microscopy (FLIM) and global analysis provide a way in which protein–protein interactions may be spatially localized and quantified within biological cells. The FRET efficiency and proportion of interacting molecules have been determined using bi-exponential fitting to time-domain FLIM data from a multiphoton time-correlated single-photon counting microscope system. The analysis has been made more robust to noise and significantly faster using global fitting, allowing higher spatial resolutions and/or lower acquisition times. Data have been simulated, as well as acquired from cell experiments, and the accuracy of a modified Levenberg–Marquardt fitting technique has been explored. Multi-image global analysis has been used to follow the epidermal growth factor-induced activation of Cdc42 in a short-image-interval time-lapse FLIM/FRET experiment. Our implementation offers practical analysis and time-resolved-image manipulation, which have been targeted towards providing fast execution, robustness to low photon counts, quantitative results and amenability to automation and batch processing.
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Affiliation(s)
- P.R Barber
- University of Oxford Gray Cancer Institute, Mount Vernon HospitalMiddlesex HA6 2JR, UK
| | - S.M Ameer-Beg
- University of Oxford Gray Cancer Institute, Mount Vernon HospitalMiddlesex HA6 2JR, UK
- King's College London, Randall CentreNew Hunt's House, Guy's Medical School Campus, London SE1 1UL, UK
| | - J Gilbey
- University of Oxford Gray Cancer Institute, Mount Vernon HospitalMiddlesex HA6 2JR, UK
| | - L.M Carlin
- King's College London, Randall CentreNew Hunt's House, Guy's Medical School Campus, London SE1 1UL, UK
| | - M Keppler
- King's College London, Randall CentreNew Hunt's House, Guy's Medical School Campus, London SE1 1UL, UK
| | - T.C Ng
- King's College London, Randall CentreNew Hunt's House, Guy's Medical School Campus, London SE1 1UL, UK
| | - B Vojnovic
- University of Oxford Gray Cancer Institute, Mount Vernon HospitalMiddlesex HA6 2JR, UK
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Fritz JV, Didier P, Clamme JP, Schaub E, Muriaux D, Cabanne C, Morellet N, Bouaziz S, Darlix JL, Mély Y, de Rocquigny H. Direct Vpr-Vpr interaction in cells monitored by two photon fluorescence correlation spectroscopy and fluorescence lifetime imaging. Retrovirology 2008; 5:87. [PMID: 18808682 PMCID: PMC2562391 DOI: 10.1186/1742-4690-5-87] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/22/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1 (HIV-1) encodes several regulatory proteins, notably Vpr which influences the survival of the infected cells by causing a G2/M arrest and apoptosis. Such an important role of Vpr in HIV-1 disease progression has fuelled a large number of studies, from its 3D structure to the characterization of specific cellular partners. However, no direct imaging and quantification of Vpr-Vpr interaction in living cells has yet been reported. To address this issue, eGFP- and mCherry proteins were tagged by Vpr, expressed in HeLa cells and their interaction was studied by two photon fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. RESULTS Results show that Vpr forms homo-oligomers at or close to the nuclear envelope. Moreover, Vpr dimers and trimers were found in the cytoplasm and in the nucleus. Point mutations in the three alpha helices of Vpr drastically impaired Vpr oligomerization and localization at the nuclear envelope while point mutations outside the helical regions had no effect. Theoretical structures of Vpr mutants reveal that mutations within the alpha-helices could perturb the leucine zipper like motifs. The DeltaQ44 mutation has the most drastic effect since it likely disrupts the second helix. Finally, all Vpr point mutants caused cell apoptosis suggesting that Vpr-mediated apoptosis functions independently from Vpr oligomerization. CONCLUSION We report that Vpr oligomerization in HeLa cells relies on the hydrophobic core formed by the three alpha helices. This oligomerization is required for Vpr localization at the nuclear envelope but not for Vpr-mediated apoptosis.
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Affiliation(s)
- Joëlle V Fritz
- Département de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7175 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Pascal Didier
- Département de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7175 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Jean-Pierre Clamme
- Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emmanuel Schaub
- Département de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7175 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Delphine Muriaux
- LaboRétro Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Charlotte Cabanne
- Ecole Supérieure de Technologie des Biomolécules de Bordeaux, Université V Ségalen, Bordeaux 2, 146, rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Nelly Morellet
- Unité de Pharmacologie Chimique et Génétique, Inserm U640 CNRS UMR8151 UFR des Sciences Pharmaceutiques et Biologiques 4, Avenue de L'observatoire, 75006 Paris, France
| | - Serge Bouaziz
- Unité de Pharmacologie Chimique et Génétique, Inserm U640 CNRS UMR8151 UFR des Sciences Pharmaceutiques et Biologiques 4, Avenue de L'observatoire, 75006 Paris, France
| | - Jean-Luc Darlix
- LaboRétro Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Yves Mély
- Département de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7175 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Hugues de Rocquigny
- Département de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7175 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
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Kofoed EM, Guerbadot M, Schaufele F. Dimerization between aequorea fluorescent proteins does not affect interaction between tagged estrogen receptors in living cells. JOURNAL OF BIOMEDICAL OPTICS 2008; 13:031207. [PMID: 18601531 PMCID: PMC2581880 DOI: 10.1117/1.2940366] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Forster resonance energy transfer (FRET) detection of protein interaction in living cells is commonly measured following the expression of interacting proteins genetically fused to the cyan (CFP) and yellow (YFP) derivatives of the Aequorea victoria fluorescent protein (FP). These FPs can dimerize at mM concentrations, which may introduce artifacts into the measurement of interaction between proteins that are fused with the FPs. Here, FRET analysis of the interaction between estrogen receptors (alpha isoform, ERalpha) labeled with "wild-type" CFP and YFP is compared with that of ERalpha labeled with "monomeric" A206K mutants of CFP and YFP. The intracellular equilibrium dissociation constant for the hormone-induced ERalpha-ERalpha interaction is similar for ERalpha labeled with wild-type or monomeric FPs. However, the measurement of energy transfer measured for ERalpha-ERalpha interaction in each cell is less consistent with the monomeric FPs. Thus, dimerization of the FPs does not affect the kinetics of ERalpha-ERalpha interaction but, when brought close together via ERalpha-ERalpha interaction, FP dimerization modestly improves FRET measurement.
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Affiliation(s)
- Eric M Kofoed
- University of California, San Francisco, Diabetes Center and Department of Medicine, S-1230, 513 Parnassus, San Francisco, California 94143-0540, USA
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Spriet C, Trinel D, Waharte F, Deslee D, Vandenbunder B, Barbillat J, Héliot L. Correlated fluorescence lifetime and spectral measurements in living cells. Microsc Res Tech 2007; 70:85-94. [PMID: 17152071 DOI: 10.1002/jemt.20385] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Studies of proteins' interaction in cells by FRET can take benefit from two important photo-physical properties describing fluorescent proteins: fluorescence emission spectrum and fluorescence lifetime. These properties provide specific and complementary information about the tagged proteins and their environment. However, none of them taken individually can completely quantify the involved fluorophore characteristics due to their multiparametric dependency with molecular environment, experimental conditions, and interpretation complexity. A solution to get a better understanding of the biological process implied at the cellular level is to combine the spectral and temporal fluorescence data acquired simultaneously at every cell region under investigation. We present the SLiM-SPRC160, an original temporal/spectral acquisition system for simultaneous lifetime measurements in 16 spectral channels directly attached to the descanned port of a confocal microscope with two-photon excitation. It features improved light throughput, enabling low-level excitation and minimum invasivity in living cells studies. To guarantee a fairly good level of accuracy and reproducibility in the measurements of fluorescence lifetime and spectra on living cells, we propose a rigorous protocol for running experiments with this new equipment that preserves cell viability. The usefulness of SLiM approach for the precise determination of overlapping fluorophores is illustrated with the study of known solutions of rhodamine. Then, we describe reliable FRET experiments in imaging mode realized in living cells using this protocol. We also demonstrate the benefit of localized fluorescence spectrum-lifetime acquisitions for the dynamic study of fluorescent proteins. proteins.
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Affiliation(s)
- Corentin Spriet
- Biophotonique Cellulaire Fonctionnelle, FRE 2963, Institut de Recherche Interdisciplinaire, 59021 Lille Cedex, France
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44
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Duncan RR. Fluorescence lifetime imaging microscopy (FLIM) to quantify protein-protein interactions inside cells. Biochem Soc Trans 2007; 34:679-82. [PMID: 17052173 PMCID: PMC1855982 DOI: 10.1042/bst0340679] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent developments in cellular imaging spectroscopy now permit the minimally invasive study of protein dynamics inside living cells. These advances are of interest to cell biologists, as proteins rarely act in isolation, but rather in concert with others in forming cellular machinery. Until recently, all protein interactions had to be determined in vitro using biochemical approaches: this biochemical legacy has provided cell biologists with the basis to test defined protein-protein interactions not only inside cells, but now also with high spatial resolution. These techniques can detect and quantify protein behaviours down to the single-molecule level, all inside living cells. More recent developments in TCSPC (time-correlated single-photon counting) imaging are now also driving towards being able to determine protein interaction rates with similar spatial resolution, and together, these experimental advances allow investigators to perform biochemical experiments inside living cells.
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Affiliation(s)
- R R Duncan
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, Scotland, UK.
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45
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Huisman A, Ploeger LS, Dullens HFJ, Beekhuis JTC, van Diest PJ. A restaining method to restore faded fluorescence in tissue specimens for quantitative confocal microscopy. Cytometry A 2007; 71:875-81. [PMID: 17622969 DOI: 10.1002/cyto.a.20432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of this study was to develop a procedure to remove the TO-PRO-3 fluorescent dye from tissue sections and restain with TO-PRO-3, still allowing calculation of DNA content and distribution by confocal laser scanning microscopy (CLSM). This would allow repeated measurements on the same tissue sections and prevents loss of tissue material from valuable clinical samples. Thick sections (14 microm) were cut from a paraffin block of adrenal tissue and stained using TO-PRO-3. Image stacks were acquired by CLSM. Thereafter, three destaining approaches were tested based on incubation, at different temperatures and durations, in the medium that is normally used to dissolve TO-PRO-3. The same areas were imaged again to measure residual fluorescence and were subsequently restained and imaged again. The intensity of the images acquired after initial staining and restaining were compared. A number of 3-D (texture) features computed after segmentation of nuclei were compared as well. The best destaining result was obtained by incubation of sections at 37 degrees C in preheated medium twice for 20 min. On average, the 3-D feature values were comparable with those after initial staining. With the described protocol it is possible to remove TO-PRO-3 fluorescence from tissue sections that can successfully be restained with minimal influence on fluorescence intensity and nuclear chromatin distribution.
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Affiliation(s)
- André Huisman
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
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46
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Medine CN, McDonald A, Bergmann A, Duncan RR. Time-correlated single photon counting FLIM: Some considerations for physiologists. Microsc Res Tech 2007; 70:420-5. [PMID: 17394229 DOI: 10.1002/jemt.20425] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recent developments in cellular imaging now permit the minimally invasive study of protein interactions in living cells. These advances are of enormous interest to cell biologists, as proteins rarely act in isolation, but rather in concert with others in forming cellular machinery. Up until recently, all protein interactions had to be determined in vitro using biochemical approaches. This biochemical legacy has provided cell biologists with the basis to test defined protein-protein interactions not only inside cells, but now also with spatial resolution. More recent developments in TCSPC imaging are now also driving towards being able to determine protein interaction rates with similar spatial resolution, and together, these experimental advances allow investigators to perform biochemical experiments inside living cells. Here, we discuss some findings we have made along the way which may be useful for physiologists to consider.
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Affiliation(s)
- Claire N Medine
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, Scotland, United Kingdom
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47
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Gan Q, Yoshida T, McDonald OG, Owens GK. Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells. Stem Cells 2006; 25:2-9. [PMID: 17023513 DOI: 10.1634/stemcells.2006-0383] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epigenetic mechanisms, such as histone modifications and DNA methylation, have been shown to play a key role in the regulation of gene transcription. Results of recent studies indicate that a novel "bivalent" chromatin structure marks key developmental genes in embryonic stem cells (ESCs), wherein a number of untranscribed lineage-control genes, such as Sox1, Nkx2-2, Msx1, Irx3, and Pax3, are epigenetically modified with a unique combination of activating and repressive histone modifications that prime them for potential activation (or repression) upon cell lineage induction and differentiation. However, results of these studies also showed that a subset of lineage-control genes, such as Myf5 and Mash1, were not marked by these histone modifications, suggesting that distinct epigenetic mechanisms might exist for lineage-control genes in ESCs. In this review article, we summarize evidence regarding possible mechanisms that control these unique histone modifications at lineage-control gene loci in ESCs and consider their possible contribution to ESC pluripotency. In addition, we propose a novel "histone modification pulsing" model wherein individual pluripotent stem cells within the inner cell mass of blastocysts undergo transient asynchronous histone modifications at these developmental gene loci, thereby conferring differential responsiveness to environmental cues and morphogenic gradients important for cell lineage determination. Finally, we consider how these rapid histone modification exchanges become progressively more stable as ESCs undergo differentiation and maturation into specialized cell lineages.
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Affiliation(s)
- Qiong Gan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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48
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Voss TC, John S, Hager GL. Single-cell analysis of glucocorticoid receptor action reveals that stochastic post-chromatin association mechanisms regulate ligand-specific transcription. Mol Endocrinol 2006; 20:2641-55. [PMID: 16873444 DOI: 10.1210/me.2006-0091] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The glucocorticoid receptor (GR) dynamically interacts with response elements in the mouse mammary tumor virus (MMTV) promoter to regulate steroid-dependent transcription. In a clonal mammary carcinoma cell line containing a tandem array of MMTV promoter-reporter gene cassettes integrated at a single genomic locus, direct binding of a green fluorescent protein (GFP)-GR fusion protein to the MMTV regulatory elements can be observed in living cells. After ligand treatment, MMTV-dependent transcription in individual cells was detected by RNA fluorescence in situ hybridization (FISH). High-resolution fluorescence images were acquired from large numbers of randomly selected cells. Images were analyzed with a novel automated computer algorithm, measuring the RNA FISH signal and the relative GFP-GR fluorescence intensity at the MMTV array for each cell. Although dexamethasone increased the mean RNA FISH signal approximately 10-fold, RU486 produced only about a 2-fold induction, as expected for this mixed antagonist. For all treatment conditions, the relative GFP-GR fluorescence at the array for the averaged cells paralleled the RNA FISH measurements, suggesting that image analysis accurately detected an increase in steady-state GR association with the MMTV array that was responsible for the increase in transcriptional activity. The antagonist-dependent decreases in GR association with the MMTV promoter were confirmed by chromatin immunoprecipitation experiments, supporting the image analysis results. A pronounced cell-to-cell variability was observed in RNA FISH signal and GR-MMTV association within treatment groups. We observed a nonlinear relationship between GR-MMTV association and RNA FISH in individual cells, indicating that differences in GR-MMTV interaction account for some, but not all, of the transcriptional heterogeneity between individual cells. In selected cell subpopulations with equal levels of GR-MMTV association, there was a decrease in RNA FISH signal with RU486 treatment compared with dexamethasone treatment. These results indicate that stochastic events occurring after GR-promoter association, such as the actions of chromatin remodeling complexes or other cofactors, change in a ligand-dependent manner and regulate heterogeneous transcription in individual cells.
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Affiliation(s)
- Ty C Voss
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
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Xia J, Kim SHH, Macmillan S, Truant R. Practical three color live cell imaging by widefield microscopy. Biol Proced Online 2006; 8:63-8. [PMID: 16909160 PMCID: PMC1523422 DOI: 10.1251/bpo119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 06/13/2006] [Accepted: 06/13/2006] [Indexed: 11/23/2022] Open
Abstract
Live cell fluorescence microscopy using fluorescent protein tags derived from jellyfish and coral species has been a successful tool to image proteins and dynamics in many species. Multi-colored aequorea fluorescent protein (AFP) derivatives allow investigators to observe multiple proteins simultaneously, but overlapping spectral properties sometimes require the use of sophisticated and expensive microscopes. Here, we show that the aequorea coerulescens fluorescent protein derivative, PS-CFP2 has excellent practical properties as a blue fluorophore that are distinct from green or red fluorescent proteins and can be imaged with standard filter sets on a widefield microscope. We also find that by widefield illumination in live cells, that PS-CFP2 is very photostable. When fused to proteins that form concentrated puncta in either the cytoplasm or nucleus, PSCFP2 fusions do not artifactually interact with other AFP fusion proteins, even at very high levels of over-expression. PSCFP2 is therefore a good blue fluorophore for distinct three color imaging along with eGFP and mRFP using a relatively simple and inexpensive microscope.
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Affiliation(s)
- Jianrun Xia
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4H24A 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada
| | - Song Hon H. Kim
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4H24A 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada
| | - Susan Macmillan
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4H24A 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4H24A 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada
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50
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Alexander MD, Burkart MD, Leonard MS, Portonovo P, Liang B, Ding X, Joullié MM, Gulledge BM, Aggen JB, Chamberlin AR, Sandler J, Fenical W, Cui J, Gharpure SJ, Polosukhin A, Zhang HR, Evans PA, Richardson AD, Harper MK, Ireland CM, Vong BG, Brady TP, Theodorakis EA, La Clair JJ. A central strategy for converting natural products into fluorescent probes. Chembiochem 2006; 7:409-16. [PMID: 16432909 DOI: 10.1002/cbic.200500466] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Matthew D Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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