1
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Basant A, Way M. The amount of Nck rather than N-WASP correlates with the rate of actin-based motility of Vaccinia virus. Microbiol Spectr 2023; 11:e0152923. [PMID: 37855608 PMCID: PMC10883800 DOI: 10.1128/spectrum.01529-23] [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: 04/11/2023] [Accepted: 09/03/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Vaccinia virus is a large double-stranded DNA virus and a close relative of Mpox and Variola virus, the causative agent of smallpox. During infection, Vaccinia hijacks its host's transport systems and promotes its spread into neighboring cells by recruiting a signaling network that stimulates actin polymerization. Over the years, Vaccinia has provided a powerful model to understand how signaling networks regulate actin polymerization. Nevertheless, we still lack important quantitative information about the system, including the precise number of viral and host molecules required to induce actin polymerization. Using quantitative fluorescence microscopy techniques, we have determined the number of viral and host signaling proteins accumulating on virions during their egress. Our analysis has uncovered two unexpected new aspects of this process: the number of viral proteins in the virion is not fixed and the velocity of virus movement depends on the level of a single adaptor within the signaling network.
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Affiliation(s)
- Angika Basant
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute , London, United Kingdom
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute , London, United Kingdom
- Department of Infectious Disease, Imperial College , London, United Kingdom
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2
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Parisutham V, Chhabra S, Ali MZ, Brewster RC. Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli. Mol Syst Biol 2022; 18:e10843. [PMID: 35694815 PMCID: PMC9189660 DOI: 10.15252/msb.202110843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/12/2022] Open
Abstract
Predicting the quantitative regulatory function of transcription factors (TFs) based on factors such as binding sequence, binding location, and promoter type is not possible. The interconnected nature of gene networks and the difficulty in tuning individual TF concentrations make the isolated study of TF function challenging. Here, we present a library of Escherichia coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation. We demonstrate the usefulness of this resource by measuring the regulatory function of the zinc‐responsive TF, ZntR, and the paralogous TF pair, GalR/GalS. For ZntR, we find that zinc alters ZntR regulatory function in a way that enables activation of the regulated gene to be robust with respect to ZntR concentration. For GalR and GalS, we are able to demonstrate that these paralogous TFs have fundamentally distinct regulatory roles beyond differences in binding affinity.
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Affiliation(s)
- Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shivani Chhabra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Robert C Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
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3
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Minaker SW, Kofoed MC, Hieter P, Stirling PC. A nuclear proteome localization screen reveals the exquisite specificity of Gpn2 in RNA polymerase biogenesis. Cell Cycle 2021; 20:1361-1373. [PMID: 34180355 DOI: 10.1080/15384101.2021.1943879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The GPN proteins are a conserved family of GTP-binding proteins that are involved in the assembly and subsequent import of RNA polymerase II and III. In this study, we sought to ascertain the specificity of yeast GPN2 for RNA polymerases by screening the localization of a collection of 1350 GFP-tagged nuclear proteins in WT or GPN2 mutant cells. We found that the strongest mislocalization occurred for RNA polymerase II and III subunits and only a handful of other RNAPII associated proteins were altered in GPN2 mutant cells. Our screen identified Ess1, an Rpb1 C-terminal domain (CTD) prolyl isomerase, as mislocalized in GPN2 mutants. Building on this observation we tested for effects of mutations in other factors which regulate Rpb1-CTD phosphorylation status. This uncovered significant changes in nuclear-cytoplasmic distribution of Rpb1-GFP in strains with disrupted RNA polymerase CTD kinases or phosphatases. Overall, this screen shows the exquisite specificity of GPN2 for RNA polymerase transport, and reveals a previously unappreciated role for CTD modification in RNAPII nuclear localization.
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Affiliation(s)
- Sean W Minaker
- Terry Fox Laboratories, BC Cancer Research Institute, Vancouver, Canada
| | - Megan C Kofoed
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
| | - Philip Hieter
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratories, BC Cancer Research Institute, Vancouver, Canada
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4
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Feng Y, Liu W, Mercadé-Prieto R, Chen XD. Dye-protein interactions between Rhodamine B and whey proteins that affect the photoproperties of the dye. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Karuna A, Masia F, Chappell S, Errington R, Hartley AM, Jones DD, Borri P, Langbein W. Quantitative Imaging of B1 Cyclin Expression Across the Cell Cycle Using Green Fluorescent Protein Tagging and Epifluorescence. Cytometry A 2020; 97:1066-1072. [PMID: 32613720 DOI: 10.1002/cyto.a.24038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 11/10/2022]
Abstract
In this article, we report the number of cyclin B1 proteins tagged with enhanced green fluorescent protein (eGFP) in fixed U-2 OS cells across the cell cycle. We use a quantitative analysis of epifluorescence to determine the number of eGFP molecules in a nondestructive way, and integrated over the cell we find 104 to 105 molecules. Based on the measured number of eGFP tagged cyclin B1 proteins, knowledge of cyclin B1 dynamics through the cell cycle, and the cell morphology, we identify the stages of cells in the cell cycle. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Arnica Karuna
- School of Physics and Astronomy, Cardiff University, Cardiff, UK
| | - Francesco Masia
- School of Physics and Astronomy, Cardiff University, Cardiff, UK.,School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | | | | | - Paola Borri
- School of Biosciences, Cardiff University, Cardiff, UK
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6
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Measurement of intracellular concentration of fluorescently-labeled targets in living cells. PLoS One 2018; 13:e0194031. [PMID: 29694385 PMCID: PMC5918622 DOI: 10.1371/journal.pone.0194031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 02/16/2018] [Indexed: 02/04/2023] Open
Abstract
Estimations of intracellular concentrations of fluorescently-labeled molecules within living cells are very important for guidance of biological experiments and interpretation of their results. Here we propose a simple and universal approach for such estimations. The approach is based upon common knowledge that the dye fluorescence is directly proportional to its quantum yield and the number of its molecules and that a coefficient of proportionality is determined by spectral properties of the dye and optical equipment used to record fluorescent signals. If two fluorescent dyes are present in the same volume, then a ratio of their concentrations is equal to a ratio of their fluorescence multiplied by some dye- and equipment-dependent coefficient. Thus, if the coefficient and concentration of one dye is known then the concentration of another dye can be determined. Here we have demonstrated how to calculate this coefficient (called a ratio factor) and how to use it for concentration measurements of fluorescently tagged molecules. As an example of how this approach can be used, we estimated a concentration of exogenously expressed neuronal Ca2+ sensor protein, hippocalcin, tagged by a fluorescent protein in a dendritic tree of rat hippocampal neurons loaded via a patch pipette with Alexa Fluor dye of known concentration. The new approach should allow performing a fast, inexpensive and reliable quantitative analysis of fluorescently-labeled targets in different parts of living cells.
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7
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Tie HC, Madugula V, Lu L. The development of a single molecule fluorescence standard and its application in estimating the stoichiometry of the nuclear pore complex. Biochem Biophys Res Commun 2016; 478:1694-9. [PMID: 27613095 DOI: 10.1016/j.bbrc.2016.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
We report here an image-based method to quantify the stoichiometry of diffraction-limited sub-cellular protein complexes in vivo under spinning disk confocal microscopy. A GFP single molecule fluorescence standard was first established by immobilizing His-tagged GFP molecules onto the glass surface via nickel nitrilotriacetic acid functionalized polyethylene glycol. When endogenous nucleoporins were knocked down and replaced by the exogenously expressed and knockdown-resistant GFP-nucleoporins, the stoichiometry of the nucleoporin was estimated by the ratio of its fluorescence intensity to that of the GFP single molecules. Our measured stoichiometry of Nup35, Nup93, Nup133 and Nup88 is 23, 18, 14 and 9 and there are possibly16 copies of Nup107-160 complex per nuclear pore complex.
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Affiliation(s)
- Hieng Chiong Tie
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Viswanadh Madugula
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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8
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Bauer M, Cubizolles F, Schmidt A, Nigg EA. Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. EMBO J 2016; 35:2152-2166. [PMID: 27539480 PMCID: PMC5048348 DOI: 10.15252/embj.201694462] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022] Open
Abstract
Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas-6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosomes is presently known. Here, we have used two complementary approaches, targeted proteomics and EGFP-tagging of centrosomal proteins at endogenous loci, to measure protein abundance in cultured human cells and purified centrosomes. Our results provide a first assessment of the absolute and relative amounts of major components of the human centrosome. Specifically, they predict that human centriolar cartwheels comprise up to 16 stacked hubs and 1 molecule of STIL for every dimer of Sas-6. This type of quantitative information will help guide future studies of the molecular basis of centrosome assembly and function.
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Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
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9
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Smirnov E, Hornáček M, Kováčik L, Mazel T, Schröfel A, Svidenská S, Skalníková M, Bartová E, Cmarko D, Raška I. Reproduction of the FC/DFC units in nucleoli. Nucleus 2016; 7:203-15. [PMID: 26934002 DOI: 10.1080/19491034.2016.1157674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units, loci of rDNA transcription and early RNA processing. In the present study we followed cell cycle related changes of these units in 2 human sarcoma derived cell lines with stable expression of RFP-PCNA (the sliding clamp protein) and GFP-RPA43 (a subunit of RNA polymerase I, pol I) or GFP-fibrillarin. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60-80%. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis, but become again active in the postmitotic daughter cells.
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Affiliation(s)
- Evgeny Smirnov
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Matúš Hornáček
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Lubomír Kováčik
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Tomáš Mazel
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Adam Schröfel
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Silvie Svidenská
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Magdalena Skalníková
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Eva Bartová
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic.,b Institute of Biophysics of the CAS , Brno , Czech Republic
| | - Dušan Cmarko
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Ivan Raška
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
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10
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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11
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Iyer S, Arindkar S, Mishra A, Manglani K, Kumar JM, Majumdar SS, Upadhyay P, Nagarajan P. Development and Evaluation of Transgenic Nude Mice Expressing Ubiquitous Green Fluorescent Protein. Mol Imaging Biol 2015; 17:471-8. [PMID: 25595814 DOI: 10.1007/s11307-014-0821-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE Researchers had developed and characterized transgenic green/red fluorescent protein (GFP/RFP) nude mouse with ubiquitous RFP or GFP expression, but none has evaluated the level of immune cells and expression levels of GFP in this model. PROCEDURE The nude GFP mice were evaluated by imaging, hematological indices, and flow cytometry to compare the proportion of immune T cells. Quantitative real-time PCR (qRT-PCR) was done for evaluating the relative expression of GFP transcripts in few organs of the nude GFP mice. RESULTS The hematological and immune cells of nude GFP were within the range of nude mice. However, the gene expression levels were relatively less in various tissues compared with B6 GFP mice. CONCLUSIONS These findings suggest that nude GFP is an ideal model resembling normal nude mice; however, GFP expression in various tissues by fluorescence should be considered, as the expression of GFP differs in various organs.
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Affiliation(s)
- Srikanth Iyer
- National Institute of Immunology, New Delhi, 110067, India
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12
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Rashidian M, Dozier JK, Distefano MD. Enzymatic labeling of proteins: techniques and approaches. Bioconjug Chem 2014; 24:1277-94. [PMID: 23837885 DOI: 10.1021/bc400102w] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Site-specific modification of proteins is a major challenge in modern chemical biology due to the large number of reactive functional groups typically present in polypeptides. Because of its importance in biology and medicine, the development of methods for site-specific modification of proteins is an area of intense research. Selective protein modification procedures have been useful for oriented protein immobilization, for studies of naturally occurring post-translational modifications, for creating antibody–drug conjugates, for the introduction of fluorophores and other small molecules on to proteins, for examining protein structure, folding, dynamics, and protein–protein interactions, and for the preparation of protein–polymer conjugates. One of the most important approaches for protein labeling is to incorporate bioorthogonal functionalities into proteins at specific sites via enzymatic reactions. The incorporated tags then enable reactions that are chemoselective, whose functional groups not only are inert in biological media, but also do not occur natively in proteins or other macromolecules. This review article summarizes the enzymatic strategies, which enable site-specific functionalization of proteins with a variety of different functional groups. The enzymes covered in this review include formylglycine generating enzyme, sialyltransferases, phosphopantetheinyltransferases, O-GlcNAc post-translational modification, sortagging, transglutaminase, farnesyltransferase, biotin ligase, lipoic acid ligase, and N-myristoyltransferase.
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13
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Kovačič M, Krč J, Lipovšek B, Topič M. Modelling of diffraction grating based optical filters for fluorescence detection of biomolecules. BIOMEDICAL OPTICS EXPRESS 2014; 5:2285-300. [PMID: 25071964 PMCID: PMC4102364 DOI: 10.1364/boe.5.002285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/30/2014] [Indexed: 06/03/2023]
Abstract
The detection of biomolecules based on fluorescence measurements is a powerful diagnostic tool for the acquisition of genetic, proteomic and cellular information. One key performance limiting factor remains the integrated optical filter, which is designed to reject strong excitation light while transmitting weak emission (fluorescent) light to the photodetector. Conventional filters have several disadvantages. For instance absorbing filters, like those made from amorphous silicon carbide, exhibit low rejection ratios, especially in the case of small Stokes' shift fluorophores (e.g. green fluorescent protein GFP with λ exc = 480 nm and λ em = 510 nm), whereas interference filters comprising many layers require complex fabrication. This paper describes an alternative solution based on dielectric diffraction gratings. These filters are not only highly efficient but require a smaller number of manufacturing steps. Using FEM-based optical modelling as a design optimization tool, three filtering concepts are explored: (i) a diffraction grating fabricated on the surface of an absorbing filter, (ii) a diffraction grating embedded in a host material with a low refractive index, and (iii) a combination of an embedded grating and an absorbing filter. Both concepts involving an embedded grating show high rejection ratios (over 100,000) for the case of GFP, but also high sensitivity to manufacturing errors and variations in the incident angle of the excitation light. Despite this, simulations show that a 60 times improvement in the rejection ratio relative to a conventional flat absorbing filter can be obtained using an optimized embedded diffraction grating fabricated on top of an absorbing filter.
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Affiliation(s)
- M. Kovačič
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška 25, Si-1000 Ljubljana, Slovenia
| | - J. Krč
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška 25, Si-1000 Ljubljana, Slovenia
| | - B. Lipovšek
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška 25, Si-1000 Ljubljana, Slovenia
| | - M. Topič
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška 25, Si-1000 Ljubljana, Slovenia
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14
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Okamoto A. Application of caged fluorescent nucleotides to live-cell RNA imaging. Methods Mol Biol 2014; 1039:303-18. [PMID: 24026705 DOI: 10.1007/978-1-62703-535-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A caged fluorescent nucleic acid probe, which contains a nucleotide modified with one photolabile nitrobenzyl unit and two hybridization-sensitive thiazole orange units, has been synthesized for area-specific fluorescence imaging of RNA in a cell. The probe emits very weak fluorescence regardless of the presence of the complementary RNA, whereas it shows hybridization-sensitive fluorescence emission after photoirradiation for uncaging. Such probes are generated via several chemical synthetic steps and are applicable to area-specific RNA imaging in a cell. Only probes that exist in the defined irradiation area are activated via uncaging irradiation.
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Affiliation(s)
- Akimitsu Okamoto
- The Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan
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15
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Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
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16
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Quantitative measurement of protein relocalization in live cells. Biophys J 2013; 104:727-36. [PMID: 23442923 DOI: 10.1016/j.bpj.2012.12.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/07/2012] [Accepted: 12/13/2012] [Indexed: 11/24/2022] Open
Abstract
Microscope cytometry provides a powerful means to study signaling in live cells. Here we present a quantitative method to measure protein relocalization over time, which reports the absolute fraction of a tagged protein in each compartment. Using this method, we studied an essential step in the early propagation of the pheromone signal in Saccharomyces cerevisiae: recruitment to the membrane of the scaffold Ste5 by activated Gβγ dimers. We found that the dose response of Ste5 recruitment is graded (EC50 = 0.44 ± 0.08 nM, Hill coefficient = 0.8 ± 0.1). Then, we determined the effective dissociation constant (K(de)) between Ste5 and membrane sites during the first few minutes when the negative feedback from the MAPK Fus3 is first activated. K(de) changed during the first minutes from a high affinity of < 0.65 nM to a steady-state value of 17 ± 9 nM. During the same period, the total number of binding sites decreased slightly, from 1940 ± 150 to 1400 ± 200. This work shows how careful quantification of a protein relocalization dynamic can give insight into the regulation mechanisms of a biological system.
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17
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Steffen PA, Fonseca JP, Gänger C, Dworschak E, Kockmann T, Beisel C, Ringrose L. Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin. Nucleic Acids Res 2013; 41:5235-50. [PMID: 23580551 PMCID: PMC3664806 DOI: 10.1093/nar/gkt217] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Polycomb (PcG) and Trithorax (TrxG) group proteins work antagonistically on several hundred developmentally important target genes, giving stable mitotic memory, but also allowing flexibility of gene expression states. How this is achieved in quantitative terms is poorly understood. Here, we present a quantitative kinetic analysis in living Drosophila of the PcG proteins Enhancer of Zeste, (E(Z)), Pleiohomeotic (PHO) and Polycomb (PC) and the TrxG protein absent, small or homeotic discs 1 (ASH1). Fluorescence recovery after photobleaching and fluorescence correlation spectroscopy reveal highly dynamic chromatin binding behaviour for all proteins, with exchange occurring within seconds. We show that although the PcG proteins substantially dissociate from mitotic chromatin, ASH1 remains robustly associated with chromatin throughout mitosis. Finally, we show that chromatin binding by ASH1 and PC switches from an antagonistic relationship in interphase, to a cooperative one during mitosis. These results provide quantitative insights into PcG and TrxG chromatin-binding dynamics and have implications for our understanding of the molecular nature of epigenetic memory.
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Affiliation(s)
- Philipp A Steffen
- Institute of Molecular Biotechnology, Dr Bohr-Gasse 3, 1030 Vienna, Austria
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18
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Coffman VC, Wu JQ. Counting protein molecules using quantitative fluorescence microscopy. Trends Biochem Sci 2012; 37:499-506. [PMID: 22948030 DOI: 10.1016/j.tibs.2012.08.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 11/24/2022]
Abstract
In recent years, quantification of absolute protein numbers in cellular structures using fluorescence microscopy has become a reality. Two popular methods are available to a broad range of researchers with minimal equipment and analysis requirements: stepwise photobleaching to count discrete changes in intensity from a small number of fluorescent fusion proteins, and comparing the fluorescence intensity of a protein to a known in vivo or in vitro standard. This review summarizes the advantages and disadvantages of each method, and gives recent examples of each that answer important questions in their respective fields. We also highlight new counting methods that could become widely available in the future.
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Affiliation(s)
- Valerie C Coffman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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19
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Mok MT, Henderson BR. The in vivo dynamic interplay of MDC1 and 53BP1 at DNA damage-induced nuclear foci. Int J Biochem Cell Biol 2012; 44:1398-409. [DOI: 10.1016/j.biocel.2012.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/16/2022]
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20
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Steffen PA, Fonseca JP, Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012; 34:901-13. [PMID: 22911103 DOI: 10.1002/bies.201200076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.
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21
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Yoshimura SH, Khan S, Ohno S, Yokogawa T, Nishikawa K, Hosoya T, Maruyama H, Nakayama Y, Takeyasu K. Site-specific attachment of a protein to a carbon nanotube end without loss of protein function. Bioconjug Chem 2012; 23:1488-93. [PMID: 22693944 DOI: 10.1021/bc300131w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Establishing a nanobiohybrid device largely relies on the availability of various bioconjugation procedures which allow coupling of biomolecules and inorganic materials. Especially, site-specific coupling of a protein to nanomaterials is highly useful and significant, since it can avoid adversely affecting the protein's function. In this study, we demonstrated a covalent coupling of a protein of interest to the end of carbon nanotubes without affecting protein's function. A modified Staudinger-Bertozzi ligation was utilized to couple a carbon nanotube end with an azide group which is site-specifically incorporated into a protein of interest. We demonstrated that Ca(2+)-sensor protein, calmodulin, can be attached to the end of the nanotubes without affecting the ability to bind to the substrate in a calcium-dependent manner. This procedure can be applied not only to nanotubes, but also to other nanomaterials, and therefore provides a fundamental technique for well-controlled protein conjugation.
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Affiliation(s)
- Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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22
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Fonseca JP, Steffen PA, Müller S, Lu J, Sawicka A, Seiser C, Ringrose L. In vivo Polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells. Genes Dev 2012; 26:857-71. [PMID: 22508729 DOI: 10.1101/gad.184648.111] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Epigenetic memory mediated by Polycomb group (PcG) proteins must be maintained during cell division, but must also be flexible to allow cell fate transitions. Here we quantify dynamic chromatin-binding properties of PH::GFP and PC::GFP in living Drosophila in two cell types that undergo defined differentiation and mitosis events. Quantitative fluorescence recovery after photobleaching (FRAP) analysis demonstrates that PcG binding has a higher plasticity in stem cells than in more determined cells and identifies a fraction of PcG proteins that binds mitotic chromatin with up to 300-fold longer residence times than in interphase. Mathematical modeling examines which parameters best distinguish stem cells from differentiated cells. We identify phosphorylation of histone H3 at Ser 28 as a potential mechanism governing the extent and rate of mitotic PC dissociation in different lineages. We propose that regulation of the kinetic properties of PcG-chromatin binding is an essential factor in the choice between stability and flexibility in the establishment of cell identities.
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23
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Mok MT, Henderson BR. The In Vivo Dynamic Organization of BRCA1-A Complex Proteins at DNA Damage-Induced Nuclear Foci. Traffic 2012; 13:800-14. [DOI: 10.1111/j.1600-0854.2012.01355.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Myth T.S. Mok
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
| | - Beric R. Henderson
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
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24
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Erlemann S, Neuner A, Gombos L, Gibeaux R, Antony C, Schiebel E. An extended γ-tubulin ring functions as a stable platform in microtubule nucleation. J Cell Biol 2012; 197:59-74. [PMID: 22472440 PMCID: PMC3317808 DOI: 10.1083/jcb.201111123] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 03/05/2012] [Indexed: 11/28/2022] Open
Abstract
γ-Tubulin complexes are essential for microtubule (MT) nucleation. The γ-tubulin small complex (γ-TuSC) consists of two molecules of γ-tubulin and one molecule each of Spc97 and Spc98. In vitro, γ-TuSCs oligomerize into spirals of 13 γ-tubulin molecules per turn. However, the properties and numbers of γ-TuSCs at MT nucleation sites in vivo are unclear. In this paper, we show by fluorescence recovery after photobleaching analysis that γ-tubulin was stably integrated into MT nucleation sites and was further stabilized by tubulin binding. Importantly, tubulin showed a stronger interaction with the nucleation site than with the MT plus end, which probably provides the basis for MT nucleation. Quantitative analysis of γ-TuSCs on single MT minus ends argued for nucleation sites consisting of approximately seven γ-TuSCs with approximately three additional γ-tubulin molecules. Nucleation and anchoring of MTs required the same number of γ-tubulin molecules. We suggest that a spiral of seven γ-TuSCs with a slight surplus of γ-tubulin nucleates MTs in vivo.
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Affiliation(s)
- Sarah Erlemann
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ–ZMBH Allianz, 69120 Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ–ZMBH Allianz, 69120 Heidelberg, Germany
| | - Linda Gombos
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ–ZMBH Allianz, 69120 Heidelberg, Germany
| | - Romain Gibeaux
- Cell Biology and Biophysics, European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Claude Antony
- Cell Biology and Biophysics, European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ–ZMBH Allianz, 69120 Heidelberg, Germany
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25
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Coffman VC, Wu P, Parthun MR, Wu JQ. CENP-A exceeds microtubule attachment sites in centromere clusters of both budding and fission yeast. ACTA ACUST UNITED AC 2012; 195:563-72. [PMID: 22084306 PMCID: PMC3257534 DOI: 10.1083/jcb.201106078] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The stoichiometries of kinetochores and their constituent proteins in yeast and vertebrate cells were determined using the histone H3 variant CENP-A, known as Cse4 in budding yeast, as a counting standard. One Cse4-containing nucleosome exists in the centromere (CEN) of each chromosome, so it has been assumed that each anaphase CEN/kinetochore cluster contains 32 Cse4 molecules. We report that anaphase CEN clusters instead contained approximately fourfold more Cse4 in Saccharomyces cerevisiae and ~40-fold more CENP-A (Cnp1) in Schizosaccharomyces pombe than predicted. These results suggest that the number of CENP-A molecules exceeds the number of kinetochore-microtubule (MT) attachment sites on each chromosome and that CENP-A is not the sole determinant of kinetochore assembly sites in either yeast. In addition, we show that fission yeast has enough Dam1-DASH complex for ring formation around attached MTs. The results of this study suggest the need for significant revision of existing CEN/kinetochore architectural models.
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Affiliation(s)
- Valerie C Coffman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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26
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Lawrimore J, Bloom KS, Salmon ED. Point centromeres contain more than a single centromere-specific Cse4 (CENP-A) nucleosome. ACTA ACUST UNITED AC 2012; 195:573-82. [PMID: 22084307 PMCID: PMC3257525 DOI: 10.1083/jcb.201106036] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Quantitative measurement of the number of Cse4, CBF3, and Ndc80 proteins at kinetochores reveals a 2.5–3-fold increased copy number relative to prior estimates. Cse4 is the budding yeast homologue of CENP-A, a modified histone H3 that specifies the base of kinetochores in all eukaryotes. Budding yeast is unique in having only one kinetochore microtubule attachment site per centromere. The centromere is specified by CEN DNA, a sequence-specific binding complex (CBF3), and a Cse4-containing nucleosome. Here we compare the ratio of kinetochore proximal Cse4-GFP fluorescence at anaphase to several standards including purified EGFP molecules in vitro to generate a calibration curve for the copy number of GFP-fusion proteins. Our results yield a mean of ∼5 Cse4s, ∼3 inner kinetochore CBF3 complexes, and ∼20 outer kinetochore Ndc80 complexes. Our calibrated measurements increase 2.5–3-fold protein copy numbers at eukaryotic kinetochores based on previous ratio measurements assuming two Cse4s per budding yeast kinetochore. All approximately five Cse4s may be associated with the CEN nucleosome, but we show that a mean of three Cse4s could be located within flanking nucleosomes at random sites that differ between chromosomes.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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27
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Newell CA, Natesan SKA, Sullivan JA, Jouhet J, Kavanagh TA, Gray JC. Exclusion of plastid nucleoids and ribosomes from stromules in tobacco and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:399-410. [PMID: 21951134 DOI: 10.1111/j.1365-313x.2011.04798.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Stromules are stroma-filled tubules that extend from the surface of plastids and allow the transfer of proteins as large as 550 kDa between interconnected plastids. The aim of the present study was to determine if plastid DNA or plastid ribosomes are able to enter stromules, potentially permitting the transfer of genetic information between plastids. Plastid DNA and ribosomes were marked with green fluorescent protein (GFP) fusions to LacI, the lac repressor, which binds to lacO-related sequences in plastid DNA, and to plastid ribosomal proteins Rpl1 and Rps2, respectively. Fluorescence from GFP-LacI co-localised with plastid DNA in nucleoids in all tissues of transgenic tobacco (Nicotiana tabacum L.) examined and there was no indication of its presence in stromules, not even in hypocotyl epidermal cells, which contain abundant stromules. Fluorescence from Rpl1-GFP and Rps2-GFP was also observed in a punctate pattern in chloroplasts of tobacco and Arabidopsis [Arabidopsis thaliana (L.) Heynh.], and fluorescent stromules were not detected. Rpl1-GFP was shown to assemble into ribosomes and was co-localised with plastid DNA. In contrast, in hypocotyl epidermal cells of dark-grown Arabidopsis seedlings, fluorescence from Rpl1-GFP was more evenly distributed in plastids and was observed in stromules on a total of only four plastids (<0.02% of the plastids observed). These observations indicate that plastid DNA and plastid ribosomes do not routinely move into stromules in tobacco and Arabidopsis, and suggest that transfer of genetic information by this route is likely to be a very rare event, if it occurs at all.
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Affiliation(s)
- Christine A Newell
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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28
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Nayak CR, Rutenberg AD. Quantification of fluorophore copy number from intrinsic fluctuations during fluorescence photobleaching. Biophys J 2011; 101:2284-93. [PMID: 22067169 DOI: 10.1016/j.bpj.2011.09.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 09/17/2011] [Accepted: 09/21/2011] [Indexed: 10/15/2022] Open
Abstract
We present a theoretical technique for quantifying the cellular copy-number of fluorophores that relies on the random nature of the photobleaching process. Our approach does not require single-molecule sensitivity, and therefore can be used with commonly used epifluorescence microscopes. Fluctuations arising from photobleaching can be used to estimate the proportionality between fluorescence intensity and copy-number, which can then be used with subsequent intensity measurements to estimate copy-number. We calculate the statistical errors of our approach and verify them with stochastic simulations. By using fluctuations over the entire photobleaching process, we obtain significantly smaller errors than previous approaches that have used fluctuations arising from cytoplasmic proteins partitioning during cellular division. From the time-dependence of the fluctuations as photobleaching proceeds, we can discriminate between desired photobleach fluctuations and background noise or photon shot noise. Our approach does not require cellular division and the photobleaching rate sets a timescale that is adjustable with respect to cellular processes. We hope that our approach will now be applied experimentally.
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Affiliation(s)
- Chitra R Nayak
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
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29
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Ikeda S, Kubota T, Wang DO, Yanagisawa H, Umemoto T, Okamoto A. Design and synthesis of caged fluorescent nucleotides and application to live-cell RNA imaging. Chembiochem 2011; 12:2871-80. [PMID: 22215304 DOI: 10.1002/cbic.201100523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Indexed: 12/23/2022]
Abstract
A binary photocontrolled nucleic acid probe that contains a nucleotide modified with one photolabile nitrobenzyl unit and two hybridization-sensitive thiazole orange units has been designed for area-specific fluorescence imaging of RNA in a cell. The synthesized probe emitted very weak fluorescence regardless of the presence of the complementary RNA, whereas it showed hybridization-sensitive fluorescence emission at 532 nm after photoirradiation at 360 or 405 nm for uncaging. Fluorescence suppression of the caged probe was attributed to a decrease in the duplex-formation ability. Caged fluorescent nucleotides with other emission wavelengths (622 and 724 nm) were also synthesized in this study; they were uncaged by 360 nm irradiation, and emitted fluorescence in the presence of the complementary RNA. Such probes were applied to area-specific RNA imaging in a cell. Only probes in the defined irradiation area were activated by uncaging irradiation, and subnuclear mRNA diffusion in a living cell was monitored.
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Affiliation(s)
- Shuji Ikeda
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
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30
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Hergeth SP, Dundr M, Tropberger P, Zee BM, Garcia BA, Daujat S, Schneider R. Isoform-specific phosphorylation of human linker histone H1.4 in mitosis by the kinase Aurora B. J Cell Sci 2011; 124:1623-8. [DOI: 10.1242/jcs.084947] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The linker histone H1 plays an essential role in maintaining and establishing higher-order chromatin structure. As with core histones, histone H1 is also extensively covalently modified. We showed previously that phosphorylation of S27 in human histone H1.4 (H1.4S27-P), prevents binding of heterochromatin protein 1 (HP1) family members (officially known as chromobox protein homologs) to the neighboring dimethylated K26. Here, we present the first functional characterization of H1.4S27-P in vivo and in vitro. We show that H1.4S27 phosphorylation is cell-cycle-regulated and its levels peak on metaphase chromosomes. We identify further Aurora B as the kinase phosphorylating H1.4S27. We demonstrate that histone H1.4 is the only somatic linker histone variant targeted by Aurora B and that Aurora B exclusively phosphorylates S27. Adjacent K26 dimethylation can regulate Aurora B activity towards S27, uncovering a crosstalk between these modifications. Finally, our fluorescence recovery after photobleaching (FRAP) analysis on histone H1.4 mutants suggests a role of S27 phosphorylation in the regulation of histone H1.4 mobility and chromatin binding in mitosis.
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Affiliation(s)
- Sonja P. Hergeth
- Max-Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago IL 60064, USA
| | - Philipp Tropberger
- Max-Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Barry M. Zee
- Department of Molecular Biology, Princeton University, Princeton NJ 08544, USA
| | - Benjamin A. Garcia
- Department of Molecular Biology, Princeton University, Princeton NJ 08544, USA
| | - Sylvain Daujat
- Max-Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Robert Schneider
- Max-Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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31
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Abstract
Now is an opportune moment to address the confluence of cell biological form and function that is the nucleus. Its arrival is especially timely because the recognition that the nucleus is extremely dynamic has now been solidly established as a paradigm shift over the past two decades, and also because we now see on the horizon numerous ways in which organization itself, including gene location and possibly self-organizing bodies, underlies nuclear functions.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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32
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Willemse J, Borst JW, de Waal E, Bisseling T, van Wezel GP. Positive control of cell division: FtsZ is recruited by SsgB during sporulation of Streptomyces. Genes Dev 2011; 25:89-99. [PMID: 21205868 DOI: 10.1101/gad.600211] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In bacteria that divide by binary fission, cell division starts with the polymerization of the tubulin homolog FtsZ at mid-cell to form a cell division scaffold (the Z ring), followed by recruitment of the other divisome components. The current view of bacterial cell division control starts from the principle of negative checkpoints that prevent incorrect Z-ring positioning. Here we provide evidence of positive control of cell division during sporulation of Streptomyces, via the direct recruitment of FtsZ by the membrane-associated divisome component SsgB. In vitro studies demonstrated that SsgB promotes the polymerization of FtsZ. The interactions are shown in vivo by time-lapse imaging and Förster resonance energy transfer and fluorescence lifetime imaging microscopy (FRET-FLIM), and are corroborated independently via two-hybrid studies. As determined by fluorescence recovery after photobleaching (FRAP), the turnover of FtsZ protofilaments increased strongly at the time of Z-ring formation. The surprising positive control of Z-ring formation by SsgB implies the evolution of an entirely new way of Z-ring control, which may be explained by the absence of a mid-cell reference point in the long multinucleoid hyphae. In turn, the localization of SsgB is mediated through the orthologous SsgA, and premature expression of the latter is sufficient to directly activate multiple Z-ring formation and hyperdivision at early stages of the Streptomyces cell cycle.
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Affiliation(s)
- Joost Willemse
- Molecular Biotechnology, Gorlaeus Laboratories, Leiden University, Leiden 2300RA, The Netherlands
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33
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Walther KA, Papke B, Sinn MB, Michel K, Kinkhabwala A. Precise measurement of protein interacting fractions with fluorescence lifetime imaging microscopy. MOLECULAR BIOSYSTEMS 2011; 7:322-36. [PMID: 21221430 DOI: 10.1039/c0mb00132e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Precise quantification of endogenous protein-protein interactions across live cells would be a major boon to biology. Such precise measurement is theoretically possible with fluorescence lifetime imaging microscopy (FLIM) but requires first properly addressing multiple biological, instrumental, statistical, and photophysical challenges. We present a detailed investigation of the last three FLIM-specific challenges. Using an efficient, highly accurate analysis code for time-domain FLIM data that accounts for all significant instrumental artifacts (in part, through use of a parametrized model for the instrument response function) and is rigorously based on both conventional statistics (full lifetime histogram fitting by χ(2) minimization) and novel statistics (single pixel fitting of lifetime populations using "maximum fidelity"), we address multiple photophysical challenges, including the proper side-by-side statistical comparison of fluorophore monoexponentiality, the precise assessment of fluorophore lifetimes and lifetime photostability, and the determination of acceptor dark state fractions. Finally, we demonstrate the feasibility of precise measurement of the interacting fraction of a protein across live cells with FLIM.
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Affiliation(s)
- Kirstin A Walther
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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34
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Haas AK, von Schwerin C, Matscheko D, Brinkmann U. Fluorescent Citrine-IgG fusion proteins produced in mammalian cells. MAbs 2010; 2:648-61. [PMID: 20724830 DOI: 10.4161/mabs.2.6.13179] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genetically encoded fluorescent antibodies are desirable for many applications in biotechnology, proteomics, microscopy, cell biology and molecular diagnostics, although efficient production of fluorescent IgGs in mammalian cells has been hampered by different and mutually incompatible secretion- and folding-requirements of antibodies and green fluorescent protein-derived fluorescent entities. Here, we show that this hurdle can be overcome by generating whole antibody fusions with Citrine, a modified yellow fluorescent protein that folds properly in the endoplasmic reticulum of mammalian cells. Applying optimized connector sequences, one or more Citrine molecules can be fused to different positions of IgGs without interfering with folding, secretion or function of the fusion proteins. These proteins can be transiently expressed and purified to similar yields as unmodified antibodies using standard technologies. IgG-Citrine fusions fully retain binding specificity and affinity, and can be applied to assays that require labeled IgG. A particularly interesting feature is the pH-dependency of Citrine fluorescence. This makes IgG-Citrine fusion proteins a valuable tool to track antibody target binding, internalization and subsequent intracellular trafficking to acidic compartments.
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35
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Zhang K, Li X, Ma Y, Zou S, Yang L, Zhang M. A curve fitting method of quantifying green fluorescent protein expression level in Escherichia coli. J Microbiol Methods 2010; 80:172-7. [DOI: 10.1016/j.mimet.2009.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 12/04/2009] [Accepted: 12/06/2009] [Indexed: 10/20/2022]
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36
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Bártová E, Horáková AH, Uhlírová R, Raska I, Galiová G, Orlova D, Kozubek S. Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments. J Histochem Cytochem 2009; 58:391-403. [PMID: 20026667 DOI: 10.1369/jhc.2009.955435] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is a nuclear compartment that plays an important role in ribosome biogenesis. Some structural features and epigenetic patterns are shared between nucleolar and non-nucleolar compartments. For example, the location of transcriptionally active mRNA on extended chromatin loop species is similar to that observed for transcriptionally active ribosomal DNA (rDNA) genes on so-called Christmas tree branches. Similarly, nucleolus organizer region-bearing chromosomes located a distance from the nucleolus extend chromatin fibers into the nucleolar compartment. Specific epigenetic events, such as histone acetylation and methylation and DNA methylation, also regulate transcription of both rRNA- and mRNA-encoding loci. Here, we review the epigenetic mechanisms and structural features that regulate transcription of ribosomal and mRNA genes. We focus on similarities in epigenetic and structural regulation of chromatin in nucleoli and the surrounding non-nucleolar region and discuss the role of proteins, such as heterochromatin protein 1, fibrillarin, nucleolin, and upstream binding factor, in rRNA synthesis and processing.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135, CZ-612 65, Brno, Czech Republic.
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37
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Green fluorescent protein – Tagged HCV non-enveloped capsid like particles: Development of a new tool for tracking HCV core uptake. Biochimie 2009; 91:903-15. [DOI: 10.1016/j.biochi.2009.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 04/15/2009] [Indexed: 12/30/2022]
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38
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George AA, Louis Schiltz R, Hager GL. Dynamic access of the glucocorticoid receptor to response elements in chromatin. Int J Biochem Cell Biol 2009; 41:214-24. [PMID: 18930837 PMCID: PMC2632576 DOI: 10.1016/j.biocel.2008.09.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 12/22/2022]
Abstract
Transcriptional activation as a rate-limiting step of gene expression is often triggered by an environmental stimulus that is transmitted through a signaling cascade to specific transcription factors. Transcription factors must then find appropriate target genes in the context of chromatin. Subsequent modulation of local chromatin domains is now recognized as a major mechanism of gene regulation. The interactions of transcription factors with chromatin structures have recently been observed to be highly dynamic, with residence times measured in seconds. Thus, the concept of static, multi-protein complexes forming at regulatory elements in the genome has been replaced by a new paradigm that envisages rapid and continuous exchange events with the template. These highly dynamic interactions are a property of both DNA-protein and protein-protein interactions and are inherent to every stage of the transcriptional response. In this review we discuss the dynamics of a nuclear receptor, and its transcriptional response in the chromatin context.
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Affiliation(s)
- Anuja A. George
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
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39
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Comparability of Fluorescence Microscopy Data and Need for Instrument Characterization of Spectral Scanning Microscopes. SPRINGER SERIES ON FLUORESCENCE 2008. [DOI: 10.1007/4243_2008_028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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40
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Dundr M, Misteli T. Measuring dynamics of nuclear proteins by photobleaching. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.5. [PMID: 18228420 DOI: 10.1002/0471143030.cb1305s18] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mobility of nuclear proteins can be studied by photobleaching techniques. The three main advantages of photobleaching are fast experimental turn around, good spatial and temporal resolution, and the ability to measure kinetics inside of living cells. The main disadvantage of these techniques is the requirement for fluorescently tagged proteins that have rigorously tested to ensure it has the same properties and function as its native counterpart. Three major methods of photobleaching microscopy are described: fluorescence recovery after photobleaching (FRAP), fluorescence loss in photobleaching (FLIP), and inverse fluorescence recovery after photobleaching (iFRAP). Each of these techniques has characteristics permitting the determination of distinct parameters of protein behavior in vivo.
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41
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Cervelli T, Palacios JA, Zentilin L, Mano M, Schwartz RA, Weitzman MD, Giacca M. Processing of recombinant AAV genomes occurs in specific nuclear structures that overlap with foci of DNA-damage-response proteins. J Cell Sci 2008; 121:349-57. [PMID: 18216333 DOI: 10.1242/jcs.003632] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Despite increasing utilization of rAAV vectors in gene transfer applications, several aspects of the biology of these vectors remain poorly understood. We have visualized the conversion of rAAV vector genomes from single-stranded to double-stranded DNA in real time. We report that rAAV DNA accumulates into discrete foci inside the nucleus. These rAAV foci are defined in number, increase in size over time after transduction, are relatively immobile, and their presence correlates with the efficiency of cell transduction. These structures overlap with, or lie in close proximity to, the foci in which proteins of the MRN (MRE11-RAD50-NBS1) complex as well as the MDC1 protein accumulate after DNA damage. The downregulation of MRN or MDC1 by RNA interference markedly increases both the formation of rAAV foci and the extent of rAAV transduction. Chromatin immunoprecipitation experiments indicate that the MRE11 protein associates with the incoming rAAV genomes and that this association decreases upon cell treatment with DNA damaging agents. These findings are consistent with a model whereby cellular DNA-damage-response proteins restrict rAAV transduction by negatively regulating rAAV genome processing.
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Affiliation(s)
- Tiziana Cervelli
- Molecular Biology Laboratory, Scuola Normale Superiore, AREA della Ricerca del CNR, Via Moruzzi 1, Pisa, Italy
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42
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Joglekar AP, Salmon ED, Bloom KS. Counting kinetochore protein numbers in budding yeast using genetically encoded fluorescent proteins. Methods Cell Biol 2008; 85:127-51. [PMID: 18155462 PMCID: PMC2892121 DOI: 10.1016/s0091-679x(08)85007-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genetically encoded fluorescent proteins are an essential tool in cell biology, widely used for investigating cellular processes with molecular specificity. Direct uses of fluorescent proteins include studies of the in vivo cellular localization and dynamics of a protein, as well as measurement of its in vivo concentration. In this chapter, we focus on the use of genetically encoded fluorescent protein as an accurate reporter of in vivo protein numbers. Using the challenge of counting the number of copies of kinetochore proteins in budding yeast as a case study, we discuss the basic considerations in developing a technique for the accurate evaluation of intracellular fluorescence signal. This discussion includes criteria for the selection of a fluorescent protein with optimal characteristics, selection of microscope and image acquisition system components, the design of a fluorescence signal quantification technique, and possible sources of measurement errors. We also include a brief survey of available calibration standards for converting the fluorescence measurements into a number of molecules, since the availability of such a standard usually determines the design of the signal measurement technique as well as the accuracy of final measurements. Finally, we show that, as in the case of budding yeast kinetochore proteins, the in vivo intracellular protein numbers determined from fluorescence measurements can also be employed to elucidate details of cellular structures.
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Affiliation(s)
- Ajit P Joglekar
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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43
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Wu JQ, McCormick CD, Pollard TD. Chapter 9 Counting Proteins in Living Cells by Quantitative Fluorescence Microscopy with Internal Standards. Methods Cell Biol 2008; 89:253-73. [DOI: 10.1016/s0091-679x(08)00609-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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44
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Mutch SA, Fujimoto BS, Kuyper CL, Kuo JS, Bajjalieh SM, Chiu DT. Deconvolving single-molecule intensity distributions for quantitative microscopy measurements. Biophys J 2007; 92:2926-43. [PMID: 17259276 PMCID: PMC1831712 DOI: 10.1529/biophysj.106.101428] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fluorescence microscopy, images often contain puncta in which the fluorescent molecules are spatially clustered. This article describes a method that uses single-molecule intensity distributions to deconvolve the number of fluorophores present in fluorescent puncta as a way to "count" protein number. This method requires a determination of the correct statistical relationship between the single-molecule and single-puncta intensity distributions. Once the correct relationship has been determined, basis histograms can be generated from the single-molecule intensity distribution to fit the puncta distribution. Simulated data were used to demonstrate procedures to determine this relationship, and to test the methodology. This method has the advantages of single-molecule measurements, providing both the mean and variation in molecules per puncta. This methodology has been tested with the avidin-biocytin binding system for which the best-fit distribution of biocytins in the sample puncta was in good agreement with a bulk determination of the avidin-biocytin binding ratio.
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Affiliation(s)
- Sarah A Mutch
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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45
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Mari PO, Florea BI, Persengiev SP, Verkaik NS, Brüggenwirth HT, Modesti M, Giglia-Mari G, Bezstarosti K, Demmers JAA, Luider TM, Houtsmuller AB, van Gent DC. Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc Natl Acad Sci U S A 2006; 103:18597-602. [PMID: 17124166 PMCID: PMC1693708 DOI: 10.1073/pnas.0609061103] [Citation(s) in RCA: 297] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand break (DSB) repair by nonhomologous end joining (NHEJ) requires the assembly of several proteins on DNA ends. Although biochemical studies have elucidated several aspects of the NHEJ reaction mechanism, much less is known about NHEJ in living cells, mainly because of the inability to visualize NHEJ repair proteins at DNA damage. Here we provide evidence that a pulsed near IR laser can produce DSBs without any visible alterations in the nucleus, and we show that NHEJ proteins accumulate in the irradiated areas. The levels of DSBs and Ku accumulation diminished in time, showing that this approach allows us to study DNA repair kinetics in vivo. Remarkably, the Ku heterodimers on DNA ends were in dynamic equilibrium with Ku70/80 in solution, showing that NHEJ complex assembly is reversible. Accumulation of XRCC4/ligase IV on DSBs depended on the presence of Ku70/80, but not DNA-PK(CS). We detected a direct interaction between Ku70 and XRCC4 that could explain these requirements. Our results suggest that this assembly constitutes the core of the NHEJ reaction and that XRCC4 may serve as a flexible tether between Ku70/80 and ligase IV.
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Affiliation(s)
- Pierre-Olivier Mari
- Departments of *Cell Biology and Genetics
- Pathology, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | - Dik C. van Gent
- Departments of *Cell Biology and Genetics
- To whom correspondence should be addressed at:
Department of Cell Biology and Genetics, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands. E-mail:
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46
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Zhang Y, Yang B. In vivo optimizing of intracellular production of heterologous protein in Pichia pastoris by fluorescent scanning. Anal Biochem 2006; 357:232-9. [PMID: 16930521 DOI: 10.1016/j.ab.2006.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 07/13/2006] [Accepted: 07/14/2006] [Indexed: 10/24/2022]
Abstract
Specific monitoring of recombinant protein titer in DNA recombinant biotechnology traditionally has relied on SDS-PAGE, Western blotting, or bioactivity-based assays, but these are labor-intensive, time-consuming, and destructive and are not a good choice for the optimization of recombinant protein production. We describe a study in which enhanced green fluorescence protein (EGFP) was fused to the C terminus of a model protein glutathione S-transferase (GST) to optimize the chimeric protein production in Pichia pastoris by measurements of fluorescence of living cells in a 96-well microtiter plate using simple fluorescent scanning. Several common factors (e.g., time course of expression, effect of methanol concentration, frequency of methanol addition, medium pH) were tested using this strategy. Western blotting assay showed that the correct full-length GST-EGFP chimeric protein was expressed intracellularly in P. pastoris. The fluorescence intensity and GST bioactivity of cell extract yielded a direct correlation. The results show that the reported method provides an attractive platform for the optimization of recombinant protein production in vivo in real time as well as handling at least 96 samples in parallel.
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Affiliation(s)
- Yaodong Zhang
- School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an 710062, China
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47
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Ghorbel S, Sinha-Datta U, Dundr M, Brown M, Franchini G, Nicot C. Human T-cell leukemia virus type I p30 nuclear/nucleolar retention is mediated through interactions with RNA and a constituent of the 60 S ribosomal subunit. J Biol Chem 2006; 281:37150-8. [PMID: 17008317 DOI: 10.1074/jbc.m603981200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Human T-cell leukemia virus type I is the etiological agent of adult T-cell leukemia/lymphoma, an aggressive and fatal lymphoproliferative malignancy. The virus has evolved strategies to escape immune clearance by remaining latent in most infected cells in vivo. We demonstrated previously that virally encoded p30 protein is a potent post-transcriptional inhibitor of virus replication (Nicot, C., Dundr, M., Johnson, J. M., Fullen, J. R., Alonzo, N., Fukumoto, R., Princler, G. L., Derse, D., Misteli, T., and Franchini, G. (2004) Nat. Med. 10, 197-201). p30 is unable to shuttle out of the nucleus in heterokaryon assays, suggesting the existence of specific retention signals. Because suppression of virus replication relies on nuclear retention of the tax/rex mRNA by p30, determining the retention features of p30 will offer hints to break latency in infected cells and insights into new therapeutic approaches. In this study, we used live cell imaging technologies to study the kinetics of p30 and to delineate its retention signals and their function in virus replication. Notably, this is the first study to identify p30 nucleolar retention domains. Using mutants of p30 that localized in different cellular compartments, we show that post-transcriptional control of virus replication by p30 occurs in the nucleoplasm. We further demonstrate that p30 nuclear/nucleolar retention is dependent upon de novo RNA transcripts and interactions with components of the ribosomal machinery.
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Affiliation(s)
- Sofiane Ghorbel
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160-7420, USA
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48
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Fernández-González R, Muñoz-Barrutia A, Barcellos-Hoff MH, Ortiz-de-Solorzano C. Quantitative in vivo microscopy: the return from the 'omics'. Curr Opin Biotechnol 2006; 17:501-10. [PMID: 16899361 DOI: 10.1016/j.copbio.2006.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 06/21/2006] [Accepted: 07/28/2006] [Indexed: 11/28/2022]
Abstract
The confluence of recent advances in microscopy instrumentation and image analysis, coupled with the widespread use of GFP-like proteins as reporters of gene expression, has opened the door to high-throughput in vivo studies that can provide the morphological and temporal context to the biochemical pathways regulating cell function. We are now able to quantify the concentration and three-dimensional distribution of multiple spectrally resolved GFP-tagged proteins. Using automatic segmentation and tracking we can then measure the dynamics of the processes in which these elements are involved. In this way, parallel studies are feasible where multiple cell colonies treated with drugs or gene expression repressors can be monitored and analyzed to study the dynamics of relevant biological processes.
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49
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Schauss AC, Bewersdorf J, Jakobs S. Fis1p and Caf4p, but not Mdv1p, determine the polar localization of Dnm1p clusters on the mitochondrial surface. J Cell Sci 2006; 119:3098-106. [PMID: 16835275 DOI: 10.1242/jcs.03026] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The mitochondrial division machinery consists of the large dynamin-related protein Dnm1p (Drp1/Dlp1 in humans), and Fis1p, Mdv1p and Caf4p. Proper assembly of Dnm1p complexes on the mitochondrial surface is crucial for balanced fission and fusion events. Using quantitative confocal microscopy, we show that Caf4p is important for the recruitment of Dnm1p to the mitochondria. The mitochondrial Dnm1p assemblies can be divided into at least two morphologically distinguishable fractions. A small subset of these assemblies appear to be present as Dnm1p-spirals (or rings) that encircle tubule constrictions, with seldom more than seven turns. A larger fraction of the Dnm1p assemblies is primarily present at one side of the mitochondrial tubules. We show that a majority of these mitochondria-associated Dnm1p clusters point towards the cell cortex. This polarized orientation is abolished in fis1Delta and caf4Delta yeast cells, but is maintained in mdv1Delta cells and after disruption of the actin cytoskeleton. This study suggests that Caf4p plays a key role in determining the polarized localization of those Dnm1p clusters that are not immediately involved in the mitochondrial fission process.
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Affiliation(s)
- Astrid C Schauss
- Max-Planck Institute for Biophysical Chemistry, Department of NanoBiophotonics, Am Fassberg 11, 37077 Göttingen, Germany
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50
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Abstract
Recently, there has been a large expansion in the usage of optical microscopes for obtaining quantitative information from biological samples in order to determine fundamental biological information such as molecular kinetics and interaction, and heterogeneity within cell populations. Consequently, we built a highly stable, uniform, isotropically emitting and convenient-to-use light source, and designed image analysis procedures for calibrating the emission light path of optical microscopes. We used the source and procedures to analyse the quantitative imaging properties of a widely used model of laser scanning confocal microscope. Results showed that the overall performance was as high as could be expected given the inherent limitations of the optical components and photomultiplier tubes. We observed that the photon detection efficiency did not vary with photomultiplier tube gain and that the highest dynamic range was achieved with relatively low gain and 12-bit digitization. Practical applications of the light source for checking the transmission of optical components in the emission light path are presented.
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Affiliation(s)
- E H Cho
- Image Analysis Laboratory, SAIC-Frederick, Inc., National Cancer Institute at Frederick, PO Box B, Frederick, Maryland 21702, USA
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